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- PDB-3rju: Crystal Structure of Beta-lactamase/D-alanine Carboxypeptidase fr... -

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Basic information

Entry
Database: PDB / ID: 3rju
TitleCrystal Structure of Beta-lactamase/D-alanine Carboxypeptidase from Yersinia pestis complexed with citrate
ComponentsBeta-lactamase/D-alanine Carboxypeptidase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta sandwich / cytosol
Function / homology
Function and homology information


: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Penicillin-binding protein / Penicillin-binding protein
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsKim, Y. / Zhou, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Beta-lactamase/D-alanine Carboxypeptidase from Yersinia pestis complexed with citrate
Authors: Kim, Y. / Zhou, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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: Beta-lactamase/D-alanine Carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1235
Polymers38,6541
Non-polymers4684
Water9,638535
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.161, 75.477, 59.068
Angle α, β, γ (deg.)90.00, 103.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase/D-alanine Carboxypeptidase / Putative penicillin-binding protein


Mass: 38654.438 Da / Num. of mol.: 1 / Fragment: UNP residues 39-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: ampH, y2964, YPO1224, YP_0915 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q7CHA2, UniProt: A0A3N4B7V6*PLUS
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.04 M potassium phosphate, 16 % w/v PEG 8000, 20 % v/v Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97903 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 18, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 57320 / Num. obs: 57320 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 12.48 Å2 / Rsym value: 0.1 / Net I/σ(I): 12
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 2041 / Rsym value: 0.615 / % possible all: 69.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
BUCCANEERmodel building
PHENIX(phenix.refine: dev_725)refinement
HKL-3000data reduction
HKL-3000data scaling
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→30.507 Å / SU ML: 0.37 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.09 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.17 2870 5.04 %random
Rwork0.138 ---
obs0.14 56939 96.84 %-
all-56939 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.299 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.065 Å20 Å2-1.5129 Å2
2---2.3155 Å2-0 Å2
3---4.3805 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2668 0 31 535 3234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092885
X-RAY DIFFRACTIONf_angle_d1.263924
X-RAY DIFFRACTIONf_dihedral_angle_d13.7741093
X-RAY DIFFRACTIONf_chiral_restr0.084431
X-RAY DIFFRACTIONf_plane_restr0.005519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.5-1.52590.32121190.25342037215674
1.5259-1.55360.2791230.21482222234580
1.5536-1.58350.23361320.19172497262990
1.5835-1.61580.20451330.16912737287098
1.6158-1.65090.20711490.15592786293599
1.6509-1.68930.18851450.14252741288699
1.6893-1.73160.18411370.13242781291899
1.7316-1.77840.1661260.132127812907100
1.7784-1.83070.2011590.124527362895100
1.8307-1.88980.1881410.120828222963100
1.8898-1.95730.16911240.118127952919100
1.9573-2.03570.14661520.12227792931100
2.0357-2.12830.16151550.125527812936100
2.1283-2.24050.18361520.126727552907100
2.2405-2.38080.16551740.128327942968100
2.3808-2.56460.16781430.126927812924100
2.5646-2.82250.17091550.136727942949100
2.8225-3.23050.15071450.137927962941100
3.2305-4.06860.13941640.130127972961100
4.0686-30.51340.15681420.15232857299999

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