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- PDB-5hwg: Structure of a cysteine hydrolase with a negative substrate -

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Basic information

Entry
Database: PDB / ID: 5hwg
TitleStructure of a cysteine hydrolase with a negative substrate
ComponentsIsochorismatase
KeywordsHYDROLASE / catalyic triad
Function / homology: / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / hydrolase activity / (1S,4R)-2-azabicyclo[2.2.1]hept-5-en-3-one / Isochorismatase
Function and homology information
Biological speciesMicrobacterium hydrocarbonoxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsFeng, Y. / Gao, S.
CitationJournal: To Be Published
Title: Structure of a cysteine hydrolase
Authors: Gao, S. / Feng, Y.
History
DepositionJan 29, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5352
Polymers20,4261
Non-polymers1091
Water2,018112
1
A: Isochorismatase
hetero molecules

A: Isochorismatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0704
Polymers40,8522
Non-polymers2182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area3270 Å2
ΔGint-18 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.291, 69.291, 86.617
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-369-

HOH

21A-390-

HOH

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Components

#1: Protein Isochorismatase


Mass: 20425.797 Da / Num. of mol.: 1 / Mutation: C111A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium hydrocarbonoxydans (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K0XHU0
#2: Chemical ChemComp-66Y / (1S,4R)-2-azabicyclo[2.2.1]hept-5-en-3-one


Mass: 109.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium malonate, 20% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 17468 / % possible obs: 98.9 % / Redundancy: 9.4 % / Net I/σ(I): 22.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→35.12 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 25.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 883 5.05 %
Rwork0.2 --
obs0.202 17468 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→35.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 8 112 1458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041377
X-RAY DIFFRACTIONf_angle_d0.8021882
X-RAY DIFFRACTIONf_dihedral_angle_d12.379480
X-RAY DIFFRACTIONf_chiral_restr0.03218
X-RAY DIFFRACTIONf_plane_restr0.004246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9926-2.11740.28461310.22392509X-RAY DIFFRACTION50
2.1174-2.28090.2491450.1992607X-RAY DIFFRACTION52
2.2809-2.51040.21331400.18422656X-RAY DIFFRACTION53
2.5104-2.87350.22991560.18882755X-RAY DIFFRACTION55
2.8735-3.61970.24261560.19912989X-RAY DIFFRACTION59
3.6197-35.12320.22941550.20443069X-RAY DIFFRACTION61

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