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- PDB-5ha8: Structure of a cysteine hydrolase -

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Basic information

Entry
Database: PDB / ID: 5ha8
TitleStructure of a cysteine hydrolase
ComponentsIsochorismatase
KeywordsHYDROLASE / catalyic triad
Function / homology: / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / hydrolase activity / Isochorismatase
Function and homology information
Biological speciesMicrobacterium hydrocarbonoxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.054 Å
AuthorsGao, S. / Feng, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31400635 China
Beijing Natural Science Foundation5154031 China
CitationJournal: To Be Published
Title: Structure of a cysteine hydrolase
Authors: Gao, S. / Feng, Y.
History
DepositionDec 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isochorismatase


Theoretical massNumber of molelcules
Total (without water)20,4581
Polymers20,4581
Non-polymers00
Water2,504139
1
A: Isochorismatase

A: Isochorismatase


Theoretical massNumber of molelcules
Total (without water)40,9162
Polymers40,9162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3260 Å2
ΔGint-18 kcal/mol
Surface area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.454, 69.454, 88.052
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

21A-311-

HOH

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Components

#1: Protein Isochorismatase / cysteine hydrolase


Mass: 20457.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium hydrocarbonoxydans (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K0XHU0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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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: 3 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6 / Details: sodium malonate (pH 6.0), polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2015
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 15793 / % possible obs: 100 % / Redundancy: 13.1 % / Net I/σ(I): 39.75

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
SCALEPACKdata scaling
RefinementResolution: 2.054→35.526 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 19.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1941 784 4.97 %
Rwork0.1709 --
obs0.172 15760 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.054→35.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1339 0 0 139 1478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041369
X-RAY DIFFRACTIONf_angle_d0.8921870
X-RAY DIFFRACTIONf_dihedral_angle_d12.718480
X-RAY DIFFRACTIONf_chiral_restr0.035216
X-RAY DIFFRACTIONf_plane_restr0.005245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0537-2.18240.24221320.19362402X-RAY DIFFRACTION99
2.1824-2.35090.20411350.18892470X-RAY DIFFRACTION100
2.3509-2.58740.21051370.18932466X-RAY DIFFRACTION100
2.5874-2.96160.24291250.19392480X-RAY DIFFRACTION100
2.9616-3.73070.19491260.18012523X-RAY DIFFRACTION100

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