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- PDB-9jyw: Crystal structure of the gamma-carbonic anhydrase from the polyex... -

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Basic information

Entry
Database: PDB / ID: 9jyw
TitleCrystal structure of the gamma-carbonic anhydrase from the polyextremophilic bacterium Aeribacillus pallidus
ComponentsGamma carbonic anhydrase family protein
KeywordsMETAL BINDING PROTEIN / gamma-class carbonic anhydrase / Zinc metalloenzyme / Aeribacillus pallidus / carbon dioxide hydration
Function / homology: / : / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / Gamma carbonic anhydrase family protein
Function and homology information
Biological speciesAeribacillus pallidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChoi, S.H. / Jin, M.S.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2022R1A2C1091278 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2024-00344154 Korea, Republic Of
CitationJournal: Mol.Cells / Year: 2024
Title: Crystal structure of gamma-carbonic anhydrase from the polyextremophilic bacterium Aeribacillus pallidus.
Authors: Choi, S.H. / Jin, M.S.
History
DepositionOct 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma carbonic anhydrase family protein
B: Gamma carbonic anhydrase family protein
C: Gamma carbonic anhydrase family protein
D: Gamma carbonic anhydrase family protein
E: Gamma carbonic anhydrase family protein
F: Gamma carbonic anhydrase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,14520
Polymers116,1686
Non-polymers97714
Water10,629590
1
A: Gamma carbonic anhydrase family protein
B: Gamma carbonic anhydrase family protein
C: Gamma carbonic anhydrase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,63811
Polymers58,0843
Non-polymers5548
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-207 kcal/mol
Surface area19300 Å2
MethodPISA
2
D: Gamma carbonic anhydrase family protein
E: Gamma carbonic anhydrase family protein
F: Gamma carbonic anhydrase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5079
Polymers58,0843
Non-polymers4236
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-205 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.911, 110.672, 98.578
Angle α, β, γ (deg.)90.00, 118.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-356-

HOH

21F-421-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Gamma carbonic anhydrase family protein


Mass: 19361.303 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeribacillus pallidus (bacteria) / Gene: AP3564_09575 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A223E5F5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris pH 7.5, 14% (w/v) polyethylene glycol 400, and 200 mM ZnSO4

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 28, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40.36 Å / Num. obs: 113523 / % possible obs: 97.6 % / Redundancy: 4.2 % / Rpim(I) all: 0.036 / Net I/σ(I): 14.9
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 47.4 / Num. unique obs: 11635 / Rpim(I) all: 0.189

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IVE

6ive


Resolution: 1.7→40.36 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.451 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / ESU R: 0.122 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24531 5934 5 %RANDOM
Rwork0.21312 ---
obs0.21475 113523 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.247 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å20.63 Å2
2---0.56 Å2-0 Å2
3----0.98 Å2
Refinement stepCycle: 1 / Resolution: 1.7→40.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7938 0 22 590 8550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138048
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177962
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.63910890
X-RAY DIFFRACTIONr_angle_other_deg1.3221.58418378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23351014
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67922.813384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.205151458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2681548
X-RAY DIFFRACTIONr_chiral_restr0.0750.21110
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028976
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021680
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6821.8294074
X-RAY DIFFRACTIONr_mcbond_other1.6811.8284073
X-RAY DIFFRACTIONr_mcangle_it2.4092.7365082
X-RAY DIFFRACTIONr_mcangle_other2.4092.7365083
X-RAY DIFFRACTIONr_scbond_it2.7692.2653972
X-RAY DIFFRACTIONr_scbond_other2.7572.2653965
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3283.2335796
X-RAY DIFFRACTIONr_long_range_B_refined7.24323.3728900
X-RAY DIFFRACTIONr_long_range_B_other7.21623.1168775
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A53430.08
12B53430.08
21A53570.08
22C53570.08
31A53240.09
32D53240.09
41A54010.07
42E54010.07
51A53770.08
52F53770.08
61B53330.08
62C53330.08
71B54250.06
72D54250.06
81B53410.09
82E53410.09
91B53520.09
92F53520.09
101C53230.09
102D53230.09
111C53570.09
112E53570.09
121C53890.07
122F53890.07
131D53290.09
132E53290.09
141D53680.09
142F53680.09
151E53970.09
152F53970.09
LS refinement shellResolution: 1.7→1.742 Å
RfactorNum. reflection% reflection
Rfree0.284 393 -
Rwork0.267 7725 -
obs--90.1 %

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