3lb9

Crystal structure of the B. circulans cpA123 circular permutant

Method: X-RAY DIFFRACTION D_max: 81.4 Å Quality: EXCELLENT

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

Endo-1,4-beta-xylanase

Bacillus circulans

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 29–146 Chain A； UniProt 152–213	Fragment：residues 65-182 and 2-63	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；13-20 % (NH4)2SO4 40 mM Tris-HCl, pH 8, VAPOR DIFFUSION, temperature 298K	Resolution 3.00 Å R-free 0.268
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 29–146 Chain B； UniProt 152–213	Fragment：residues 65-182 and 2-63	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；13-20 % (NH4)2SO4 40 mM Tris-HCl, pH 8, VAPOR DIFFUSION, temperature 298K	Resolution 3.00 Å R-free 0.268
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 29–146 Chain C； UniProt 152–213	Fragment：residues 65-182 and 2-63	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；13-20 % (NH4)2SO4 40 mM Tris-HCl, pH 8, VAPOR DIFFUSION, temperature 298K	Resolution 3.00 Å R-free 0.268

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 3LB9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BCX MUTATIONAL AND CRYSTALLOGRAPHIC ANALYSES OF THE ACTIVE SITE RESIDUES OF THE BACILLUS CIRCULANS XYLANASE Deposited 1994-04-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.81 Å
1BVV SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE Deposited 1998-09-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.80 Å
1C5H HYDROGEN BONDING AND CATALYSIS: AN UNEXPECTED EXPLANATION FOR HOW A SINGLE AMINO ACID SUBSTITUTION CAN CHANGE THE PH OPTIMUM OF A GLYCOSIDASE Deposited 1999-11-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa） Fragment：CATALYTIC DOMAIN	Mutation：N35D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.55 Å
1C5I HYDROGEN BONDING AND CATALYSIS: AN UNEXPECTED EXPLANATION FOR HOW A SINGLE AMINO ACID SUBSTITUTION CAN CHANGE THE PH OPTIMUM OF A GLYCOSIDASE Deposited 1999-11-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa） Fragment：CATALYTIC DOMAIN	Mutation：N35D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.80 Å
1HV0 DISSECTING ELECTROSTATIC INTERACTIONS AND THE PH-DEPENDENT ACTIVITY OF A FAMILY 11 GLYCOSIDASE Deposited 2001-01-05	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa） Fragment：Y80F_BCX	Mutation：Y80F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；ammonimu sulphate, sodium chloride, TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298 K	Resolution 1.60 Å
1HV1 DISSECTING ELECTROSTATIC INTERACTIONS AND THE PH-DEPENDENT ACTIVITY OF A FAMILY 11 GLYCOSIDASE Deposited 2001-01-05	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa） Fragment：Q127A_BCX	Mutation：Q127A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；ammonimu sulphate, sodium chloride, TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298 K	Resolution 1.80 Å
1XNB HIGH-RESOLUTION STRUCTURES OF XYLANASES FROM B. CIRCULANS AND T. HARZIANUM IDENTIFY A NEW FOLDING PATTERN AND IMPLICATIONS FOR THE ATOMIC BASIS OF THE CATALYSIS Deposited 1994-06-01	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 29–213（185 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.49 Å
1XNC THERMOSTABILIZATION OF THE BACILLUS CIRCULANS XYLANASE, BY THE INTRODUCTION OF DISULFIDE BONDS Deposited 1994-06-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å
2BVV SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE. Deposited 1998-11-17	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：Y69F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.50 Å
3VZJ Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) E172H mutant Deposited 2012-10-14	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 29–213（185 aa）	Mutation：E172H	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.41 Å R-free 0.343
3VZJ Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) E172H mutant Deposited 2012-10-14	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：E172H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.41 Å R-free 0.343
3VZJ Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) E172H mutant Deposited 2012-10-14	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 29–213（185 aa）	Mutation：E172H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.41 Å R-free 0.343
3VZJ Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) E172H mutant Deposited 2012-10-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 29–213（185 aa）	Mutation：E172H	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.41 Å R-free 0.343
3VZK Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35E mutant Deposited 2012-10-14	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：N35E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.55 Å R-free 0.197
3VZK Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35E mutant Deposited 2012-10-14	Different construct 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 29–213（185 aa）	Mutation：N35E	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.55 Å R-free 0.197
3VZL Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35H mutant Deposited 2012-10-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：N35H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.266
3VZL Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35H mutant Deposited 2012-10-15	Different construct 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 29–213（185 aa）	Mutation：N35H	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.266
3VZL Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35H mutant Deposited 2012-10-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 29–213（185 aa）	Mutation：N35H	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.266
3VZL Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35H mutant Deposited 2012-10-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 29–213（185 aa）	Mutation：N35H	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.266
3VZM Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) E172H mutant with Glu78 covalently bonded to 2-deoxy-2-fluoro-xylobiose Deposited 2012-10-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E172H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.86 Å R-free 0.254
3VZN Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35E mutant with Glu78 covalently bonded to 2-deoxy-2-fluoro-xylobiose Deposited 2012-10-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：N35E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.67 Å R-free 0.236
3VZN Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35E mutant with Glu78 covalently bonded to 2-deoxy-2-fluoro-xylobiose Deposited 2012-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：N35E	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.67 Å R-free 0.236
3VZO Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35H mutant with Glu78 covalently bonded to 2-deoxy-2-fluoro-xylobiose Deposited 2012-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：N35H	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.73 Å R-free 0.200
7VUG Cryo-EM structure of a class A orphan GPCR in complex with Gi Deposited 2021-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 29–213（185 aa）	Mutation：D39F, R150D, S62V	7ZQ 3-chloranyl-N-[2-oxidanylidene-2-[[(1S)-1-phenylethyl]amino]ethyl]benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7VUH Cryo-EM structure of a class A orphan GPCR Deposited 2021-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 29–213（185 aa）	Mutation：D39F, R150D, S62V	7ZQ 3-chloranyl-N-[2-oxidanylidene-2-[[(1S)-1-phenylethyl]amino]ethyl]benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
7VUI Cryo-EM structure of a class A orphan GPCR Deposited 2021-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 29–213（185 aa）	Mutation：D39F, R150D, S62V	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 7ZQ 3-chloranyl-N-[2-oxidanylidene-2-[[(1S)-1-phenylethyl]amino]ethyl]benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7VUJ Cryo-EM structure of a class A orphan GPCR Deposited 2021-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 29–213（185 aa）	Mutation：D39F, R150D, S62V	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 7ZQ 3-chloranyl-N-[2-oxidanylidene-2-[[(1S)-1-phenylethyl]amino]ethyl]benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7XN9 Crystal structure of SSTR2 and L-054,522 complex Deposited 2022-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GI9 tert-butyl (2S)-6-azanyl-2-[[(2R,3S)-3-(1H-indol-3-yl)-2-[[4-(2-oxidanylidene-3H-benzimidazol-1-yl)piperidin-1-yl]carbonylamino]butanoyl]amino]hexanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293 K；100-400 mM lithium nitrate, 6-10% PEG2000, 100 mM L-054,522, and 0.1 M HEPES, pH 7.0	Resolution 2.60 Å R-free 0.265
7XNA Crystal structure of somatostatin receptor 2 (SSTR2) with peptide antagonist CYN 154806 Deposited 2022-04-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 29–213（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293 K；100-300 mM ammonium sulphate, 6-10% PEG2000, 1 mg/ml CYN 154806, and 0.1 M HEPES, pH 7.0	Resolution 2.65 Å R-free 0.290
8QXY Xylanase from Bacillus circulans mutant E78Q bound to xylotriose Deposited 2023-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E78Q	ZN ZINC ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；5 %v/v PEGSB, 0.071 M Zn Acet, 0.1 M BIS-TRIS, 0.2 M LiSO4	Resolution 1.41 Å R-free 0.211
8QXY Xylanase from Bacillus circulans mutant E78Q bound to xylotriose Deposited 2023-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：E78Q	ZN ZINC ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；5 %v/v PEGSB, 0.071 M Zn Acet, 0.1 M BIS-TRIS, 0.2 M LiSO4	Resolution 1.41 Å R-free 0.211
8QXZ Xylanase from Bacillus circulans mutant E78Q/Y69A Deposited 2023-10-25	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 29–213（185 aa）	Mutation：E78Q, Y69A	ZN ZINC ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；10 %v/v PEGSB, 0.2 M LiSO4, BIS-TRIS, pH 7.5	Resolution 1.50 Å R-free 0.183
8QXZ Xylanase from Bacillus circulans mutant E78Q/Y69A Deposited 2023-10-25	Different construct 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 29–213（185 aa）	Mutation：E78Q, Y69A	ZN ZINC ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；10 %v/v PEGSB, 0.2 M LiSO4, BIS-TRIS, pH 7.5	Resolution 1.50 Å R-free 0.183
8QY0 Xylanase from Bacillus circulans mutant E78Q/Y69A bound to xylotriose Deposited 2023-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E78Q, Y69A	ZN ZINC ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；25 %v/v PEGSB, 0.2 M LiSO4, 0.05 M Zn Acet, 0.1 M BIS-TRIS 7.5 pH	Resolution 1.90 Å R-free 0.197
8QY0 Xylanase from Bacillus circulans mutant E78Q/Y69A bound to xylotriose Deposited 2023-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：E78Q, Y69A	ZN ZINC ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；25 %v/v PEGSB, 0.2 M LiSO4, 0.05 M Zn Acet, 0.1 M BIS-TRIS 7.5 pH	Resolution 1.90 Å R-free 0.197
8QY1 Xylanase from Bacillus circulans mutant E78Q/Y69A bound to xylohexaose Deposited 2023-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E78Q, Y69A	ZN ZINC ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；22.5 %v/v PEGSB, 0.2 M LiSO4, 0.1 M BIS-TRIS 7.5 pH	Resolution 1.90 Å R-free 0.238
8QY1 Xylanase from Bacillus circulans mutant E78Q/Y69A bound to xylohexaose Deposited 2023-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：E78Q, Y69A	ZN ZINC ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；22.5 %v/v PEGSB, 0.2 M LiSO4, 0.1 M BIS-TRIS 7.5 pH	Resolution 1.90 Å R-free 0.238
8QY2 Xylanase from Bacillus circulans mutant E78Q/F125A Deposited 2023-10-25	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 29–213（185 aa）	Mutation：E78Q, F125A	GOL GLYCEROL × 3 ZN ZINC ION × 2 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；22.5 %v/v PEGSB, 0.2 M LiSO4, 0.05 M Zn Acet, 0.1 M BIS-TRIS pH 7.5	Resolution 1.70 Å R-free 0.214
8QY3 Xylanase from Bacillus circulans mutant E78Q/F125A bound to xylotriose Deposited 2023-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E78Q, F125A	ZN ZINC ION × 2 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 1 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；22.5 %v/v PEGSB, 0.2 M LiSO4, 0.05 M Zn Acetate, 0.1 M BIS-TRIS, pH 7.5	Resolution 1.24 Å R-free 0.230
8R85 Xylanase from Bacillus circulans mutant E78Q/W9A Deposited 2023-11-28	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 29–213（185 aa）	Mutation：E78Q, W9A	GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；18.182 %v/v PEGSH 0.1 M BICINE 9.16 pH	Resolution 1.30 Å R-free 0.172
8R86 Xylanase from Bacillus circulans mutant E78Q/W71A Deposited 2023-11-28	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E78Q, W71A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20.727 %v/v PEGSH, 0.1 M BICINE 8.81 pH	Resolution 1.50 Å R-free 0.173
8R86 Xylanase from Bacillus circulans mutant E78Q/W71A Deposited 2023-11-28	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：E78Q, W71A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20.727 %v/v PEGSH, 0.1 M BICINE 8.81 pH	Resolution 1.50 Å R-free 0.173
9M42 Structure-based discovery of potent agonists of the orphan receptor GPR139 Deposited 2025-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 27–213（187 aa）	Not recorded	A1L8O 2-[5-(4-methylthiophen-3-yl)-1,2,4-oxadiazol-3-yl]-~{N}-[(1~{S})-1-phenylethyl]ethanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9W0H S1P3 in complex with cpd-32 and spm242 Deposited 2025-07-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–213（185 aa） Fragment：H137Y, C84S, D39F, R150D	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.268
9W0L S1P3 in complex with CYM52581 and spm242 Deposited 2025-07-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–213（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.60 Å R-free 0.281

32 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	XYNA_BACCI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 65–182； UniProt 29–146 Author chain A； PDBConstruct 2–63； UniProt 152–213 Author chain B； PDBConstruct 65–182； UniProt 29–146 Author chain B； PDBConstruct 2–63； UniProt 152–213 Author chain C； PDBConstruct 65–182； UniProt 29–146 Author chain C； PDBConstruct 2–63； UniProt 152–213

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	3lb9
Deposition date deposition_date	2010-01-08
Structure title title	Crystal structure of the B. circulans cpA123 circular permutant
Keywords keywords	permutation, BcX, Glycosidase, Xylan degradation, HYDROLASE; HYDROLASE
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	26.26 Å
Radius of gyration Rg (electron density) rg_electron	25.63 Å
Forward intensity I(0) i0	62595700.00
Molecular weight molecular_weight	59897.0 kDa
Excluded volume excluded_volume	73874 Å³
Envelope volume envelope_volume	87893 Å³
Hydration-shell volume shell_volume	28791 Å³
Envelope diameter envelope_diameter	86.6 Å
Shell Rg shell_rg	32.64 Å
Envelope Rg envelope_rg	25.67 Å
Shape Rg shape_rg	25.60 Å
Total Rg total_rg	26.43 Å
Total atoms total_atoms	4254
Residues n_residues	546
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	81.4 Å
Rg (real space) rg_real	26.18 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	6.2600e+07
I(0) uncertainty (real space) i0_real_error	1.0090e+06
Rg (reciprocal space) rg_reciprocal	26.21 Å
I(0) (reciprocal space) i0_reciprocal	62600000.0000
Solution quality estimate total_estimate	0.9085
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.1 Å
Skewness Skewness skewness	0.212
Kurtosis Kurtosis kurtosis	-0.588
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19110000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3lb9A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	180 — Glycoside hydrolase family 11/12, catalytic domain

Domain ID domain_id	3lb9B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	180 — Glycoside hydrolase family 11/12, catalytic domain

Domain ID domain_id	3lb9C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	180 — Glycoside hydrolase family 11/12, catalytic domain

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8. Citations (1)

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Unit-cell length a length_a	69.810 Å
Unit-cell length b length_b	114.970 Å
Unit-cell length c length_c	65.030 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.47 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	19.880 Å
R factor r_factor	0.1950
R_work r_work	0.1920
R_free r_free	0.2680

Description description	Endo-1,4-beta-xylanase
Molecular weight formula_weight	19991.6 kDa
EC 编号 ec_number	3.2.1.8
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4294

Crystal structure of the B. circulans cpA123 circular permutant

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

Endo-1,4-beta-xylanase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Bacillus circulans
NCBI Class编号 ncbi_taxonomy_id	1397
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	40

fit	/app/data/saxs_computation/lb/3lb9/3lb9.fit
pddf	/app/data/pr_computation/lb/3lb9/3lb9.pr.out
profile	/app/data/saxs_computation/lb/3lb9/3lb9.dat