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5k7j

Structure of designed zinc binding protein ZE2 bound to Zn2+

Method: X-RAY DIFFRACTION Dmax: 81.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Indole-3-glycerol phosphate synthase

Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

UniProt Q06121

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 A； UniProt 2–248 Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.10 M succinate 22% PEG 3350 Resolution 1.39 Å R-free 0.230
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 2–248 Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.10 M succinate 22% PEG 3350 Resolution 1.39 Å R-free 0.230

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 5K7J Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A53 COMPLEX OF INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS WITH INDOLE-3-GLYCEROLPHOSPHATE AT 2.0 A RESOLUTION Deposited 1998-02-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–248（247 aa）
Not recorded IGP INDOLE-3-GLYCEROL PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；pH 5.5
Resolution 2.00 Å R-free 0.212
1IGS INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS AT 2.0 A RESOLUTION Deposited 1995-08-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–248（248 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；pH 5.
Resolution 2.00 Å
1JUK INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS IN A TRIGONAL CRYSTAL FORM Deposited 1996-05-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–248（248 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；pH 6.0
Resolution 2.50 Å
1JUL INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS IN A SECOND ORTHORHOMBIC CRYSTAL FORM Deposited 1996-05-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–248（248 aa）
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.00 Å
1LBF CRYSTAL STRUCTURE OF INDOLE-3-GLYCEROL PHOSPHATE SYNTASE (IGPS)WITH REDUCED 1-(O-CABOXYPHENYLAMINO)-1-DEOXYRIBULOSE 5-PHOSPHATE (RCDRP) Deposited 2002-04-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–248（247 aa）
Not recorded 137 1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；30% ammonium sulphate, 50 mM phosphate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.05 Å R-free 0.225
1LBL Crystal structure of indole-3-glycerol phosphate synthase (IGPS) in complex with 1-(o-carboxyphenylamino)-1-deoxyribulose 5'-phosphate (CdRP) Deposited 2002-04-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–248（247 aa）
Not recorded 137 1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；279 K；1.2M ammonium sulphate, 50 mM potassium phosphate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 2.40 Å R-free 0.247
2C3Z Crystal structure of a truncated variant of indole-3-glycerol phosphate synthase from Sulfolobus solfataricus Deposited 2005-10-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–248（222 aa） Fragment：DELTA(1-26), RESIDUES 27-248
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 30% PEG8000 0.2 M AMMONIUM SULFATE 0.1 M MES, PH 6.5
Resolution 2.80 Å
3NYZ Crystal Structure of Kemp Elimination Catalyst 1A53-2 Deposited 2010-07-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–248（248 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1 bis-tris, 0.2 M ammonium acetate, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.51 Å R-free 0.251
3NYZ Crystal Structure of Kemp Elimination Catalyst 1A53-2 Deposited 2010-07-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–248（248 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1 bis-tris, 0.2 M ammonium acetate, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.51 Å R-free 0.251
3NZ1 Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole Deposited 2010-07-15 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 1–248（248 aa）
Mutation：E51A, S81A, L83A, K110W, L131A, L157A, E159V, G178E, N180A, E210W, S211Q, L231G 3NY 5-nitro-1H-benzotriazole × 1 SO4 SULFATE ION × 6 TLA L(+)-TARTARIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；0.2 potassium sodium tartrate, 2M ammonium sulfate, 0.1 M sodium citrate/citric acid, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.56 Å R-free 0.210
3TC6 Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR63. Deposited 2011-08-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–247（247 aa）
Not recorded PO4 PHOSPHATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions Microbatch crystallization under oil；pH 5；277 K；40% PEG 400, 0.1 M Sodium phosphate monobasic, 0.1 M Sodium acetate, pH 5.0, Microbatch crystallization under oil, temperature 277K
Resolution 1.60 Å R-free 0.198
3TC7 Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR62. Deposited 2011-08-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–247（247 aa）
Not recorded PO4 PHOSPHATE ION × 3 ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions Microbatch crystallization under oil；pH 5；277 K；40 % PEG 400, 0.1 M Ammonium phosphate monobasic, 0.1 M Sodium acetate, pH 5.0, Microbatch crystallization under oil, temperature 277K
Resolution 1.50 Å R-free 0.193
4A2R Structure of the engineered retro-aldolase RA95.5-5 Deposited 2011-09-28 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 1–245（245 aa） Fragment：TIM-BARREL FOLD, RESIDUES 1-245
Mutation：YES 3NK 1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；301 K；0.1 M TRIS PH 8.5, 0.2 M NA2HPO4, 23% W/V PEG3350, 28 DEGREES CELSIUS.
Resolution 1.30 Å R-free 0.165
4A2S Structure of the engineered retro-aldolase RA95.5 Deposited 2011-09-28 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 1–245（245 aa） Fragment：TIM-BARREL FOLD, RESIDUES 1-245
Mutation：YES 3NK 1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；301 K；0.1 M HEPES KOH PH 7.6, 23% W/V PEG 3350,20 MM NA2HPO4, 28 DEG. CELSIUS.
Resolution 1.40 Å R-free 0.162
4IWW Computational Design of an Unnatural Amino Acid Metalloprotein with Atomic Level Accuracy Deposited 2013-01-24 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 2–248（247 aa）
Mutation：K10E, F22V, S70A, K110M, I133BPA, N161T, N179T, R181Q, L183D, E209D, F246L Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 6 CO COBALT (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；1.8 M ammonium sulfate, 5% PEG3350, pH 6.5, EVAPORATION, temperature 298K
Resolution 2.30 Å R-free 0.264
4IWW Computational Design of an Unnatural Amino Acid Metalloprotein with Atomic Level Accuracy Deposited 2013-01-24 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 2–248（247 aa）
Mutation：K10E, F22V, S70A, K110M, I133BPA, N161T, N179T, R181Q, L183D, E209D, F246L Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 CO COBALT (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；1.8 M ammonium sulfate, 5% PEG3350, pH 6.5, EVAPORATION, temperature 298K
Resolution 2.30 Å R-free 0.264
4IX0 Computational Design of an Unnatural Amino Acid Metalloprotein with Atomic Level Accuracy Deposited 2013-01-24 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 2–248（247 aa）
Mutation：K10E, F22V, S70A, K110M, I133BPA, N161T, N179T, R181Q, L183D, E209D, F246L Non-standard monomer：Yes (specific site not provided by mmCIF) NI NICKEL (II) ION × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；1.6 M ammonium sulfate, 3% PEG3350, pH 6.5, EVAPORATION, temperature 298K
Resolution 2.50 Å R-free 0.257
5AOU Structure of the engineered retro-aldolase RA95.5-8F apo Deposited 2015-09-11 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 1–245（245 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 5 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；293 K；0.1M SODIUM ACETATE TRIHYDRATE, 2M AMMONIUM SULFATE, PH 4.6, 20DEGREE CELSIUS
Resolution 1.10 Å R-free 0.219
6NW4 Evolution of a computationally designed Kemp eliminase Deposited 2019-02-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–248（247 aa）
Not recorded SO4 SULFATE ION × 4 6NT 6-NITROBENZOTRIAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate, 20 mM sodium sulfate, 43% v/v PEG 300, pH 5.6
Resolution 3.00 Å R-free 0.295

17 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRPC_SULSO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–249； UniProt 2–248 Author chain B； PDBConstruct 3–249； UniProt 2–248

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

SAXS profile for 5k7j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5k7j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5k7j
Deposition date deposition_date2016-05-26
Structure title titleStructure of designed zinc binding protein ZE2 bound to Zn2+
Keywords keywordsMetalloprotein, Designed, TIM barrel, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.38 Å
Radius of gyration Rg (electron density) rg_electron25.52 Å
Forward intensity I(0) i047804500.00
Molecular weight molecular_weight55001.0 kDa
Excluded volume excluded_volume69672 ų
Envelope volume envelope_volume83993 ų
Hydration-shell volume shell_volume27765 ų
Envelope diameter envelope_diameter82.7 Å
Shell Rg shell_rg32.34 Å
Envelope Rg envelope_rg25.50 Å
Shape Rg shape_rg25.51 Å
Total Rg total_rg26.35 Å
Total atoms total_atoms3868
Residues n_residues483
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax81.0 Å
Rg (real space) rg_real26.42 Å
Rg uncertainty (real space) rg_real_error0.41 Å
I(0) (real space) i0_real4.7800e+07
I(0) uncertainty (real space) i0_real_error6.2850e+05
Rg (reciprocal space) rg_reciprocal26.41 Å
I(0) (reciprocal space) i0_reciprocal47800000.0000
Solution quality estimate total_estimate0.8941
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.4 Å
Skewness Skewness skewness0.372
Kurtosis Kurtosis kurtosis-0.530
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18560000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.896
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id5k7jA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id5k7jB00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
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8. Citations (1)

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9. Files and Curves (10)