2ofm

1.11 A Crystal Structure of Apo Nitrophorin 4 From Rhodnius Prolixus

Method: X-RAY DIFFRACTION D_max: 49.5 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nitrophorin-4

Rhodnius prolixus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain X； UniProt 22–205	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；300 K；ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K	Resolution 1.11 Å R-free 0.183

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2OFM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D2U 1.15 A CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS Deposited 1999-09-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa） Fragment：RESIDUES 22-205	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NH3 AMMONIA × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；3.0 M AMMONIUM PHOSPHATE 10 MM TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.15 Å R-free 0.190
1D3S 1.4 A crystal structure of nitrophorin 4 from Rhodnius prolixis at pH=5.6. Deposited 1999-09-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa） Fragment：RESIDUES 22-205	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；23% PEG 4000 20 MM SODIUM CITRATE PH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.40 Å R-free 0.250
1EQD CRYSTAL STRUCTURE OF NITROPHORIN 4 COMPLEXED WITH CN Deposited 2000-04-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	CYN CYANIDE ION × 1 HEV 5,8-DIMETHYL-1,2,3,4-TETRAVINYLPORPHINE-6,7-DIPROPIONIC ACID FERROUS COMPLEX × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；PEG 4000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.260
1ERX CRYSTAL STRUCTURE OF NITROPHORIN 4 COMPLEXED WITH NO Deposited 2000-04-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEV 5,8-DIMETHYL-1,2,3,4-TETRAVINYLPORPHINE-6,7-DIPROPIONIC ACID FERROUS COMPLEX × 1 NO NITRIC OXIDE × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；PEG 4000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.40 Å R-free 0.240
1IKE Crystal Structure of Nitrophorin 4 from Rhodnius Prolixus Complexed with Histamine at 1.5 A Resolution Deposited 2001-05-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HSM HISTAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；PEG4000, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.50 Å R-free 0.240
1IKJ 1.27 A CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS COMPLEXED WITH IMIDAZOLE Deposited 2001-05-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；PEG-4000, sodium citrate, pH 5.60, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.27 Å R-free 0.173
1KOI CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS COMPLEXED WITH NITRIC OXIDE AT 1.08 A RESOLUTION Deposited 2001-05-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；PEG 4000, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.08 Å R-free 0.147
1ML7 Crystal structure of nitrophorin 4 complexed with 4-iodopyrazole Deposited 2002-08-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEV 5,8-DIMETHYL-1,2,3,4-TETRAVINYLPORPHINE-6,7-DIPROPIONIC ACID FERROUS COMPLEX × 1 PYZ 4-IODOPYRAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；ammonium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K, temperature 298.0K	Resolution 1.25 Å R-free 0.194
1NP4 CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS Deposited 1998-07-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NH3 AMMONIA × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；2.8 M AMMONIUM PHOSPHATE, 0.1 M NA CACODYLATE, PH 5.6 (FINAL PH 7.5), ROOM TEMPERATURE	Resolution 1.50 Å R-free 0.262
1SXU 1.4 A Crystal Structure of D30N Mutant of Nitrophorin 4 from Rhodnius Prolixus Complexed with Imidazole Deposited 2004-03-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Mutation：D30N	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.40 Å R-free 0.175
1SXW 1.05 A Crystal Structure of D30A Mutant of Nitrophorin 4 from Rhodnius Prolixus Complexed with Nitric Oxide Deposited 2004-03-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Mutation：D30A	PO4 PHOSPHATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Ammonium Phosphate 3.2 M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.05 Å R-free 0.179
1SXX 1.0 A Crystal Structure of D129A/L130A Mutant of Nitrophorin 4 Complexed with Nitric Oxide Deposited 2004-03-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Mutation：D129A, L130A	PO4 PHOSPHATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Ammonium Phosphate 3.2 M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.01 Å R-free 0.155
1SXY 1.07 A Crystal Structure of D30N Mutant of Nitrophorin 4 from Rhodnius Prolixus Deposited 2004-03-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Mutation：D30N	NH4 AMMONIUM ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Ammonium Phosphate 3.2 M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.07 Å R-free 0.172
1SY0 1.15 A Crystal Structure of T121V Mutant of Nitrophorin 4 from Rhodnius Prolixus Deposited 2004-03-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Mutation：T121V	NH4 AMMONIUM ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Ammonium Phosphate 3.2 M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.15 Å R-free 0.172
1SY1 1.0 A Crystal Structure of T121V Mutant of Nitrophorin 4 Complexed with Nitric Oxide Deposited 2004-03-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Mutation：T121V	PO4 PHOSPHATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Ammonium Phosphate 3.2 M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.01 Å R-free 0.145
1SY2 1.0 A Crystal Structure of D129A/L130A Mutant of Nitrophorin 4 Deposited 2004-03-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Mutation：D129A, L130A	NH4 AMMONIUM ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Ammonium Phosphate 2.8 M, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.00 Å R-free 0.170
1SY3 1.00 A Crystal Structure of D30N Mutant of Nitrophorin 4 from Rhodnius Prolixus Complexed with Nitric Oxide Deposited 2004-03-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Mutation：D30N	PO4 PHOSPHATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Ammonium Phosphate 3.2 M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.00 Å R-free 0.159
1U0X Crystal structure of nitrophorin 4 under pressure of xenon (200 psi) Deposited 2004-07-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NH3 AMMONIA × 1 XE XENON × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；ammonium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.45 Å R-free 0.175
1X8N 1.08 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Complexed With Nitric Oxide at pH 7.4 Deposited 2004-08-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；300 K；ammonium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K	Resolution 1.08 Å R-free 0.171
1X8O 1.01 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Complexed With Nitric Oxide at pH 5.6 Deposited 2004-08-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	PO4 PHOSPHATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；300 K；ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K	Resolution 1.01 Å R-free 0.130
1X8P 0.85 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Complexed With Ammonia at pH 7.4 Deposited 2004-08-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NH3 AMMONIA × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；300 K；ammonium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K	Resolution 0.85 Å R-free 0.159
1X8Q 0.85 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus in Complex with Water at pH 5.6 Deposited 2004-08-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；300 K；PEG 4000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K	Resolution 0.85 Å R-free 0.130
1YWA 0.9 A Structure of NP4 from Rhodnius Prolixus complexed with CO at pH 5.6 Deposited 2005-02-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	PO4 PHOSPHATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CMO CARBON MONOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；2.8 M ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 0.89 Å R-free 0.150
1YWB 0.9 A Structure of NP4 from Rhodnius Prolixus complexed with NO at pH 5.6 Deposited 2005-02-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	PO4 PHOSPHATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；2.8 M ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 0.97 Å R-free 0.170
1YWC Structure of the ferrous CO complex of NP4 from Rhodnius Prolixus at pH 7.0 Deposited 2005-02-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CMO CARBON MONOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.8 M ammonium phosphate, pH 7., VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.00 Å R-free 0.150
1YWD 1.08 A Structure of Ferrous NP4 (aquo complex) Deposited 2005-02-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；2.8 M ammonium phosphate, pH 7.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.08 Å R-free 0.170
2AT0 1.00 A Crystal Structure Of L133V Mutant of Nitrophorin 4 From Rhodnius Prolixus Complexed With Nitric Oxide at pH 5.6 Deposited 2005-08-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 22–205（184 aa）	Mutation：L133V	PO4 PHOSPHATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；300 K；ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K	Resolution 1.00 Å R-free 0.154
2AT3 1.00 A Crystal Structure Of L123V/L133V Mutant of Nitrophorin 4 From Rhodnius Prolixus Complexed With Imidazole at pH 5.6 Deposited 2005-08-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 22–205（184 aa）	Mutation：L123V, L133V	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；300 K；ammonium phosphate, imidazole, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K	Resolution 1.00 Å R-free 0.167
2AT5 1.22 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Containing Fe(III) Deuteroporphyrin IX Complexed With Nitric Oxide at pH 5.6 Deposited 2005-08-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 22–205（184 aa）	Not recorded	PO4 PHOSPHATE ION × 1 FDE FE(III) DEUTEROPORPHYRIN IX × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；300 K；ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K	Resolution 1.22 Å R-free 0.148
2AT6 1.22 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Containing Fe(III) Deuteroporphyrin IX Complexed With Water at pH 5.6 Deposited 2005-08-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 22–205（184 aa）	Not recorded	FDE FE(III) DEUTEROPORPHYRIN IX × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；300 K；ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K	Resolution 1.22 Å R-free 0.167
2AT8 0.96 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Containing Fe(III) 2,4 Dimethyl Deuteroporphyrin IX Complexed With Nitric Oxide at pH 5.6 Deposited 2005-08-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 22–205（184 aa）	Not recorded	PO4 PHOSPHATE ION × 1 FDD FE(III) 2,4-DIMETHYL DEUTEROPORPHYRIN IX × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；300 K；ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K	Resolution 1.00 Å R-free 0.195
2OFR 1.00 A Crystal Structure Of V36A/D129A/L130A Mutant of Nitrophorin 4 From Rhodnius Prolixus Complexed With Nitric Oxide at pH 5.6 Deposited 2007-01-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 22–205（184 aa）	Not recorded	PO4 PHOSPHATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；300 K；ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.00 Å R-free 0.148
3C76 1.07 A crystal structure of L133V mutant of nitrophorin 4 from Rhodnius prolixus complexed with ammonia at PH 7.5 Deposited 2008-02-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 22–205（184 aa）	Mutation：L133V	NH3 AMMONIA × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；AMMONIUM PHOSPHATE, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K	Resolution 1.07 Å R-free 0.165
3C77 1.08 A crystal structure of nitrophorin 4 from Rhodnius prolixus containing FE(III) deuteroporphyrin ix complexed with ammonia at ph 7.5 Deposited 2008-02-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 22–205（184 aa）	Not recorded	NH3 AMMONIA × 1 FDE FE(III) DEUTEROPORPHYRIN IX × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；AMMONIUM PHOSPHATE, pH 7.50, temperature 300.0K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.08 Å R-free 0.162
3C78 0.98 A crystal structure of nitrophorin 4 from Rhodnius prolixus containing FE(III) 2,4 dimethyl deuteroporphyrin ix complexed with ammonia at ph 7.5 Deposited 2008-02-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 22–205（184 aa）	Not recorded	NH3 AMMONIA × 1 FDD FE(III) 2,4-DIMETHYL DEUTEROPORPHYRIN IX × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；AMMONIUM PHOSPHATE, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K	Resolution 0.98 Å R-free 0.189
3FLL Crystal structure of E55Q mutant of nitrophorin 4 Deposited 2008-12-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa） Fragment：UNP residues 22-205	Mutation：E55Q	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NH3 AMMONIA × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.50 Å R-free 0.201
3MVF Crystal Structure of Nitrophorin 4 from Rhodnius prolixus Complexed with Nitrite at pH 7.4 Deposited 2010-05-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO2 NITRITE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；297 K；Ammonium phosphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 1.40 Å R-free 0.187
3MVF Crystal Structure of Nitrophorin 4 from Rhodnius prolixus Complexed with Nitrite at pH 7.4 Deposited 2010-05-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NO2 NITRITE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；297 K；Ammonium phosphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 1.40 Å R-free 0.187
3TGA Crystal structure of L130R mutant of Nitrophorin 4 from Rhodnius prolixus at pH 7.4 Deposited 2011-08-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Mutation：L130R	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；297 K；Ammonium phosphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 1.30 Å R-free 0.172
3TGB Crystal structure of L130R mutant of Nitrophorin 4 from Rhodnius prolixus complexed with imidazole at pH 7.4 Deposited 2011-08-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Mutation：L130R	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；297 K；Ammonium phosphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 1.35 Å R-free 0.186
3TGC Crystal structure of L130R mutant of Nitrophorin 4 from Rhodnius prolixus complexed with nitrite at pH 7.4 Deposited 2011-08-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Mutation：L130R	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO2 NITRITE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；297 K；Ammonium phosphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 1.40 Å R-free 0.187
4GNW Crystal structure of nitrophorin 4 triple mutant complex with ammonia Deposited 2012-08-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Mutation：D30N, E32Q, D35N	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NH3 AMMONIA × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.85 M ammonium phosphate, 100 mM Tris.HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.15 Å R-free 0.181
4GNW Crystal structure of nitrophorin 4 triple mutant complex with ammonia Deposited 2012-08-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 22–205（184 aa）	Mutation：D30N, E32Q, D35N	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NH3 AMMONIA × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.85 M ammonium phosphate, 100 mM Tris.HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.15 Å R-free 0.181
4GRJ Crystal structure of nitrophorin 4 triple mutant complex with NO Deposited 2012-08-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Mutation：D30N, E32Q, D35N	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.85 M ammonium phosphate, 100 mM Tris.HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.15 Å R-free 0.185
4GRJ Crystal structure of nitrophorin 4 triple mutant complex with NO Deposited 2012-08-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 22–205（184 aa）	Mutation：D30N, E32Q, D35N	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.85 M ammonium phosphate, 100 mM Tris.HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.15 Å R-free 0.185
4HPA Crystal structure of Nitrophorin 4 from Rhodnius prolixus Complexed with sulfide ion at pH 7.4 Deposited 2012-10-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；3.2M AMMONIUM PHOSPHATE, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.50 Å R-free 0.181
4HPB Crystal structure of Nitrophorin 4 from Rhodnius prolixus Complexed with Beta-Mercaptoethanol at pH 7.4 Deposited 2012-10-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；3.2M AMMONIUM PHOSPHATE, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.179
4HPC Crystal structure of Nitrophorin 4 from Rhodnius prolixus Complexed with Cysteine at pH 7.4 Deposited 2012-10-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYS CYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；3.2M AMMONIUM PHOSPHATE, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.40 Å R-free 0.169
4HPD Crystal structure of Nitrophorin 4 from Rhodnius prolixus Complexed with homocysteine at pH 7.4 Deposited 2012-10-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HCS 2-AMINO-4-MERCAPTO-BUTYRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；3.2M AMMONIUM PHOSPHATE, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.30 Å R-free 0.179
5HWZ Crystal structure of nitrophorin 4 D30N mutant with nitrite Deposited 2016-01-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–205（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO2 NITRITE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；Potassium phosphate	Resolution 1.45 Å R-free 0.180

47 other PDB entries and 50 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NP4_RHOPR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 1–184； UniProt 22–205

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2ofm
Deposition date deposition_date	2007-01-03
Structure title title	1.11 A Crystal Structure of Apo Nitrophorin 4 From Rhodnius Prolixus
Keywords keywords	lipocalin, beta barrel, absent cofactor, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	16.64 Å
Radius of gyration Rg (electron density) rg_electron	15.22 Å
Forward intensity I(0) i0	8017760.00
Molecular weight molecular_weight	20361.0 kDa
Excluded volume excluded_volume	25359 Å³
Envelope volume envelope_volume	29011 Å³
Hydration-shell volume shell_volume	15660 Å³
Envelope diameter envelope_diameter	47.9 Å
Shell Rg shell_rg	21.59 Å
Envelope Rg envelope_rg	15.42 Å
Shape Rg shape_rg	15.16 Å
Total Rg total_rg	16.52 Å
Total atoms total_atoms	1433
Residues n_residues	184
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	49.5 Å
Rg (real space) rg_real	16.50 Å
Rg uncertainty (real space) rg_real_error	0.15 Å
I(0) (real space) i0_real	8.0180e+06
I(0) uncertainty (real space) i0_real_error	8.5390e+04
Rg (reciprocal space) rg_reciprocal	16.51 Å
I(0) (reciprocal space) i0_reciprocal	8018000.0000
Solution quality estimate total_estimate	0.8986
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.1 Å
Skewness Skewness skewness	-0.007
Kurtosis Kurtosis kurtosis	-0.449
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2473000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Nitrophorin-4
Molecular weight formula_weight	20292.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	2322

ACTKNAIAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKEALYHYDPKTQDTFYDVSELQVESLGKYTANFKKVDKNGNVKVAVTAGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDAAAGDKVKSAVSAATLEFSKFISTKENNCAYDNDSLKSLLTK

来源 Source

来源生物 organism	Rhodnius prolixus
NCBI Class编号 ncbi_taxonomy_id	13249
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	408

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2ofmx_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.1 — Retinol binding protein-like

CATH v4.4 (1 domains)

Domain ID domain_id	2ofmX00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

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8. Citations (1)

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Unit-cell length a length_a	69.470 Å
Unit-cell length b length_b	42.816 Å
Unit-cell length c length_c	52.720 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.71 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.110 Å
Low-resolution limit resolution_low	17.400 Å
R factor r_factor	0.1480
R_work r_work	0.1462
R_free r_free	0.1827

fit	/app/data/saxs_computation/of/2ofm/2ofm.fit
pddf	/app/data/pr_computation/of/2ofm/2ofm.pr.out
profile	/app/data/saxs_computation/of/2ofm/2ofm.dat