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- PDB-3ksr: CRYSTAL STRUCTURE OF A PUTATIVE SERINE HYDROLASE (XCC3885) FROM X... -

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Basic information

Entry
Database: PDB / ID: 3ksr
TitleCRYSTAL STRUCTURE OF A PUTATIVE SERINE HYDROLASE (XCC3885) FROM XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS AT 2.69 A RESOLUTION
ComponentsPutative serine hydrolase
KeywordsHYDROLASE / SERINE HYDROLASE / CATALYTIC TRIAD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


serine-type endopeptidase activity
Similarity search - Function
Rhinovirus 14, subunit 4 - #100 / Rhinovirus 14, subunit 4 / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Other non-globular / Special / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold ...Rhinovirus 14, subunit 4 - #100 / Rhinovirus 14, subunit 4 / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Other non-globular / Special / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Hydrolase or peptidase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris str. ATCC 33913 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.69 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of Putative serine hydrolase (NP_639225.1) from XANTHOMONAS CAMPESTRIS at 2.69 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2524
Polymers32,0261
Non-polymers2253
Water18010
1
A: Putative serine hydrolase
hetero molecules

A: Putative serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5038
Polymers64,0532
Non-polymers4516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4550 Å2
ΔGint-68 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.865, 56.865, 220.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Putative serine hydrolase /


Mass: 32026.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris str. ATCC 33913 (bacteria)
Gene: XCC3885 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8P431
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.64
Details: 1.82M di-ammonium hydrogen phosphate, 0.2M sodium chloride, 0.1M Imidazole pH 7.64, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97849
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 26, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 2.69→39.559 Å / Num. obs: 10299 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 81.766 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 17.22
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.69-2.790.6931.331621642183.2
2.79-2.90.5512.144491704189.5
2.9-3.030.4353.265681852197.9
3.03-3.190.2465.567531855197.6
3.19-3.390.149.570671886197.3
3.39-3.650.0881571001832197.2
3.65-4.010.05322.873521850196.7
4.01-4.590.03631.473741847196.1
4.59-5.750.03136.474141840195.8
5.75-39.5590.02642.274671853193.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.69→39.559 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 21.998 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.498 / ESU R Free: 0.271
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. PHOSPHATE (PO4) AND CHLORIDE (CL) MODELLED ARE PRESENT IN CRYSTALLIZATION CONDITION. ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. PHOSPHATE (PO4) AND CHLORIDE (CL) MODELLED ARE PRESENT IN CRYSTALLIZATION CONDITION. 4. RAMACHANDRAN OUTLIER (G242) IS LIKELY DUE TO POOR QUALITY OF THE MAPS AT THIS LOCATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 497 4.8 %RANDOM
Rwork0.197 ---
obs0.198 10275 95.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.68 Å2 / Biso mean: 45.347 Å2 / Biso min: 20.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--0.55 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.69→39.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 11 10 1878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211905
X-RAY DIFFRACTIONr_bond_other_d0.0020.021242
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9632595
X-RAY DIFFRACTIONr_angle_other_deg0.97533027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4885242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73223.73583
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76415301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0271513
X-RAY DIFFRACTIONr_chiral_restr0.0810.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212141
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
X-RAY DIFFRACTIONr_mcbond_it1.40531207
X-RAY DIFFRACTIONr_mcbond_other0.2653492
X-RAY DIFFRACTIONr_mcangle_it2.61751927
X-RAY DIFFRACTIONr_scbond_it5.158698
X-RAY DIFFRACTIONr_scangle_it7.15111668
LS refinement shellResolution: 2.691→2.761 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 42 -
Rwork0.369 677 -
all-719 -
obs--92.18 %
Refinement TLS params.Method: refined / Origin x: 13.466 Å / Origin y: 12.2514 Å / Origin z: 66.9184 Å
111213212223313233
T0.2135 Å2-0.0927 Å2-0.0868 Å2-0.0861 Å20.0448 Å2--0.1219 Å2
L1.2317 °20.5999 °20.702 °2-1.4436 °21.358 °2--1.6784 °2
S-0.1264 Å °0.1757 Å °0.0937 Å °-0.1466 Å °0.1428 Å °-0.1726 Å °-0.2296 Å °0.1408 Å °-0.0165 Å °

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