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- PDB-3s6j: The crystal structure of a hydrolase from Pseudomonas syringae -

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Basic information

Entry
Database: PDB / ID: 3s6j
TitleThe crystal structure of a hydrolase from Pseudomonas syringae
ComponentsHydrolase, haloacid dehalogenase-like family
KeywordsHYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


sugar-phosphatase activity / metal ion binding
Similarity search - Function
: / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...: / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Hydrolase, haloacid dehalogenase-like family
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.198 Å
AuthorsZhang, Z. / Syed Ibrahim, B. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of a hydrolase from Pseudomonas syringae
Authors: Zhang, Z. / Syed Ibrahim, B. / Burley, S.K. / Swaminathan, S.
History
DepositionMay 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2011Group: Structure summary
Revision 1.2Jan 29, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn / struct_ref_seq_dif
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydrolase, haloacid dehalogenase-like family
B: Hydrolase, haloacid dehalogenase-like family
C: Hydrolase, haloacid dehalogenase-like family
D: Hydrolase, haloacid dehalogenase-like family
E: Hydrolase, haloacid dehalogenase-like family
F: Hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,79815
Polymers156,4376
Non-polymers3619
Water4,648258
1
A: Hydrolase, haloacid dehalogenase-like family
E: Hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2665
Polymers52,1462
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-44 kcal/mol
Surface area18610 Å2
MethodPISA
2
B: Hydrolase, haloacid dehalogenase-like family
F: Hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2665
Polymers52,1462
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-44 kcal/mol
Surface area18340 Å2
MethodPISA
3
C: Hydrolase, haloacid dehalogenase-like family
D: Hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2665
Polymers52,1462
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-43 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.535, 74.887, 75.113
Angle α, β, γ (deg.)59.77, 67.49, 88.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Hydrolase, haloacid dehalogenase-like family


Mass: 26072.820 Da / Num. of mol.: 6 / Fragment: UNP residues 105-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Gene: PSPTO0276, PSPTO_0276 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-coden+RIL(p)-Stratagene / References: UniProt: Q88AV7
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Calcium chloride, 0.1 M HEPES, 28% PEG400, 0.1 M EDTA, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 59117 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.5
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.7 / % possible all: 93.1

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.198→49.89 Å / SU ML: 0.31 / Isotropic thermal model: Isotropic / σ(F): 0.13 / Phase error: 26.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 2816 5.05 %
Rwork0.1952 --
obs0.1977 55731 92.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.354 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.6844 Å26.1935 Å2-9.4962 Å2
2---7.388 Å21.3708 Å2
3---4.7036 Å2
Refinement stepCycle: LAST / Resolution: 2.198→49.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9944 0 9 258 10211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910092
X-RAY DIFFRACTIONf_angle_d1.21213660
X-RAY DIFFRACTIONf_dihedral_angle_d18.4253706
X-RAY DIFFRACTIONf_chiral_restr0.081590
X-RAY DIFFRACTIONf_plane_restr0.0051752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1975-2.23540.30731080.22382162X-RAY DIFFRACTION75
2.2354-2.27610.31461160.20832309X-RAY DIFFRACTION81
2.2761-2.31980.24331350.1942408X-RAY DIFFRACTION84
2.3198-2.36720.27381260.19812507X-RAY DIFFRACTION88
2.3672-2.41870.2591560.20612629X-RAY DIFFRACTION91
2.4187-2.47490.27991540.20552629X-RAY DIFFRACTION93
2.4749-2.53680.31191160.21032629X-RAY DIFFRACTION93
2.5368-2.60540.27181490.19132720X-RAY DIFFRACTION94
2.6054-2.68210.23641460.1852707X-RAY DIFFRACTION94
2.6821-2.76860.26111410.18472751X-RAY DIFFRACTION95
2.7686-2.86760.27081330.19592713X-RAY DIFFRACTION95
2.8676-2.98240.24211500.20432688X-RAY DIFFRACTION95
2.9824-3.11810.27571500.19132756X-RAY DIFFRACTION96
3.1181-3.28240.22871630.18842734X-RAY DIFFRACTION96
3.2824-3.4880.25051570.18822751X-RAY DIFFRACTION96
3.488-3.75730.22061390.18152761X-RAY DIFFRACTION96
3.7573-4.13520.211550.1662733X-RAY DIFFRACTION96
4.1352-4.73320.20371480.17352752X-RAY DIFFRACTION96
4.7332-5.96180.25461350.21252781X-RAY DIFFRACTION97
5.9618-49.90280.22761390.21922795X-RAY DIFFRACTION97

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