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- PDB-3irv: CRYSTAL STRUCTURE OF CYSTEINE HYDROLASE PSPPH_2384 FROM Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 3irv
TitleCRYSTAL STRUCTURE OF CYSTEINE HYDROLASE PSPPH_2384 FROM Pseudomonas syringae pv. phaseolicola 1448A
ComponentsCYSTEINE HYDROLASE
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / CYSTEINE HYDROLASE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC
Function / homology
Function and homology information


: / Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Isochorismatase family protein
Similarity search - Component
Biological speciesPseudomonas syringae pv. phaseolicola 1448A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsPatskovsky, Y. / Malashkevich, V. / Toro, R. / Foti, R. / Dickey, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF CYSTEINE HYDROLASE PSPPH_2384 FROM Pseudomonas syringae
Authors: Patskovsky, Y. / Malashkevich, V. / Toro, R. / Foti, R. / Dickey, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionAug 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 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: CYSTEINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0763
Polymers25,8881
Non-polymers1872
Water4,972276
1
A: CYSTEINE HYDROLASE
hetero molecules

A: CYSTEINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1516
Polymers51,7772
Non-polymers3744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area5870 Å2
ΔGint-51 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.477, 67.477, 178.343
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-261-

PO4

21A-16-

HOH

31A-327-

HOH

41A-371-

HOH

51A-381-

HOH

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Components

#1: Protein CYSTEINE HYDROLASE / Isochorismatase family protein


Mass: 25888.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. phaseolicola 1448A (bacteria)
Gene: PSPPH_2384 / Production host: Escherichia coli (E. coli) / References: UniProt: Q48J46
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M SODIUM PHOSPHATE-CITRATE, PH 4.2, 10% ISOPROPANOL, 200MM LITHIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 32614 / % possible obs: 100 % / Observed criterion σ(I): -5 / Redundancy: 5.5 % / Biso Wilson estimate: 17.17 Å2 / Rsym value: 0.13 / Net I/σ(I): 3.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.385 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18955 1028 3.2 %RANDOM
Rwork0.15933 ---
obs0.16028 31391 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.032 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1652 0 11 276 1939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221758
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.9662407
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0815232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52523.33381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46315303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4321518
X-RAY DIFFRACTIONr_chiral_restr0.1020.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021327
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.3832
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.51222
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.5413
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.360
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.594
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.55221119
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.45831798
X-RAY DIFFRACTIONr_scbond_it4.6263704
X-RAY DIFFRACTIONr_scangle_it6.5995599
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.601→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 85 -
Rwork0.24 2193 -
obs--97.43 %

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