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- PDB-4pw0: Alpha/beta hydrolase fold protein from Chitinophaga pinensis -

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Basic information

Entry
Database: PDB / ID: 4pw0
TitleAlpha/beta hydrolase fold protein from Chitinophaga pinensis
ComponentsAlpha/beta hydrolase fold protein
KeywordsHYDROLASE / structural genomics / APC103277 / alpha/beta hydrolase fold protein / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologyalpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Alpha/beta hydrolase fold protein
Function and homology information
Biological speciesChitinophaga pinensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.48 Å
AuthorsOsipiuk, J. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Alpha/beta hydrolase fold protein from Chitinophaga pinensis.
Authors: Osipiuk, J. / Tesar, C. / Clancy, S. / Joachimiak, A.
History
DepositionMar 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Alpha/beta hydrolase fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1227
Polymers31,9091
Non-polymers2136
Water6,738374
1
A: Alpha/beta hydrolase fold protein
hetero molecules

A: Alpha/beta hydrolase fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,24314
Polymers63,8182
Non-polymers42512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
Buried area3380 Å2
ΔGint-133 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.380, 110.380, 59.184
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Alpha/beta hydrolase fold protein


Mass: 31908.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chitinophaga pinensis (bacteria) / Strain: DSM 2588 / Gene: Cpin_2213 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C7PEX8
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 3.26 Å3/Da / Density % sol: 62.29 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 3 M NaCl, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2014
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.48→37.2 Å / Num. all: 133991 / Num. obs: 133991 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.244 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.48-1.513.70.6211.8666770.65499.9
1.51-1.534.20.57266510.662100
1.53-1.564.60.5267700.689100
1.56-1.594.70.4766890.744100
1.59-1.634.80.42266970.774100
1.63-1.6750.39367210.82100
1.67-1.715.10.37566820.862100
1.71-1.755.20.35167290.942100
1.75-1.815.40.31266971.024100
1.81-1.865.40.24466791.078100
1.86-1.935.40.19767241.227100
1.93-2.015.40.14766831.366100
2.01-2.15.40.12467261.466100
2.1-2.215.40.10367071.537100
2.21-2.355.40.09367211.59100
2.35-2.535.40.08666661.649100
2.53-2.795.40.08567241.762100
2.79-3.195.30.07566791.795100
3.19-4.025.20.05467091.8199.9
4.02-505.20.04666601.76799

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.48→37.2 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.428 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.041 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1333 3453 5.1 %RANDOM
Rwork0.1035 ---
obs0.105 68260 99.83 %-
all-68260 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.62 Å2 / Biso mean: 22.607 Å2 / Biso min: 7.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å20 Å2
2---0.03 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.48→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 6 374 2550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192449
X-RAY DIFFRACTIONr_bond_other_d0.0010.022294
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9593379
X-RAY DIFFRACTIONr_angle_other_deg0.89835312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08324.173127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4415393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9331516
X-RAY DIFFRACTIONr_chiral_restr0.1130.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212896
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02610
X-RAY DIFFRACTIONr_mcbond_it1.8021.9311170
X-RAY DIFFRACTIONr_mcbond_other1.8011.9311169
X-RAY DIFFRACTIONr_mcangle_it1.8452.9091478
X-RAY DIFFRACTIONr_rigid_bond_restr3.79834743
X-RAY DIFFRACTIONr_sphericity_free36.297591
X-RAY DIFFRACTIONr_sphericity_bonded9.7254944
LS refinement shellResolution: 1.481→1.52 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 257 -
Rwork0.161 4704 -
all-4961 -
obs-4961 98.94 %

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