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- PDB-5evi: Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase fr... -

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Basic information

Entry
Database: PDB / ID: 5evi
TitleCrystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase from Pseudomonas syringae
Components(Beta-Lactamase/D-Alanine ...) x 4
KeywordsHYDROLASE / alpha-beta-fold / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / 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
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, Y. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase from Pseudomonas syringae
Authors: Kim, Y. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionNov 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_reflns_twin / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_reflns_twin.operator / _pdbx_struct_oper_list.symmetry_operation

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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
B: Beta-Lactamase/D-Alanine Carboxypeptidase
C: Beta-Lactamase/D-Alanine Carboxypeptidase
D: Beta-Lactamase/D-Alanine Carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,81917
Polymers162,7744
Non-polymers1,04513
Water9,188510
1
A: Beta-Lactamase/D-Alanine Carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9414
Polymers40,6871
Non-polymers2543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-Lactamase/D-Alanine Carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8453
Polymers40,6871
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-Lactamase/D-Alanine Carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0656
Polymers40,6871
Non-polymers3785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-Lactamase/D-Alanine Carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9684
Polymers40,7141
Non-polymers2543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.869, 72.645, 93.770
Angle α, β, γ (deg.)89.94, 90.01, 90.08
Int Tables number1
Space group name H-MP1

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Components

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Beta-Lactamase/D-Alanine ... , 4 types, 4 molecules ABCD

#1: Protein Beta-Lactamase/D-Alanine Carboxypeptidase


Mass: 40686.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: ampC, PSPTO_3594 / Plasmid: pMCSG73 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q87Z37, beta-lactamase
#2: Protein Beta-Lactamase/D-Alanine Carboxypeptidase


Mass: 40686.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: ampC, PSPTO_3594 / Plasmid: pMCSG73 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q87Z37, beta-lactamase
#3: Protein Beta-Lactamase/D-Alanine Carboxypeptidase


Mass: 40686.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: ampC, PSPTO_3594 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q87Z37, beta-lactamase
#4: Protein Beta-Lactamase/D-Alanine Carboxypeptidase


Mass: 40713.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: ampC, PSPTO_3594 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q87Z37, beta-lactamase

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Non-polymers , 3 types, 523 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 45.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2.0 M Ammonium Sulfate 0.1 M Bis-Tris:HCl pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2015
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.323
11-h,-k,l20.284
11h,-k,-l30.206
11-H, K, -L40.187
ReflectionResolution: 1.8→50 Å / Num. all: 128402 / Num. obs: 128402 / % possible obs: 97.5 % / Redundancy: 2.2 % / Rsym value: 0.054 / Net I/σ(I): 12.44
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.49 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→36.32 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.753 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20081 5791 4.7 %RANDOM
Rwork0.16316 ---
obs0.16493 117229 92.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.853 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20.1 Å20.05 Å2
2---1.78 Å2-3.19 Å2
3---2.98 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11118 0 59 510 11687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01911532
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211001
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.98215724
X-RAY DIFFRACTIONr_angle_other_deg0.972325227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12951452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57724.563515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.866151646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2161564
X-RAY DIFFRACTIONr_chiral_restr0.080.21775
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113286
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022674
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6262.1365781
X-RAY DIFFRACTIONr_mcbond_other1.6262.1365780
X-RAY DIFFRACTIONr_mcangle_it2.8333.1987242
X-RAY DIFFRACTIONr_mcangle_other2.8333.1987243
X-RAY DIFFRACTIONr_scbond_it1.52.2945751
X-RAY DIFFRACTIONr_scbond_other1.52.2945751
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6573.3888483
X-RAY DIFFRACTIONr_long_range_B_refined5.37617.17912845
X-RAY DIFFRACTIONr_long_range_B_other5.34517.13512742
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.796→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 283 -
Rwork0.2 5967 -
obs--63.74 %
Refinement TLS params.Method: refined / Origin x: 20.1943 Å / Origin y: 13.7246 Å / Origin z: 23.793 Å
111213212223313233
T0.0147 Å20.0014 Å20.0049 Å2-0.029 Å2-0.0056 Å2--0.0485 Å2
L0.0087 °20.005 °2-0.0054 °2-0.0154 °2-0.0079 °2--0.0201 °2
S-0.0008 Å °0.0157 Å °-0.0029 Å °-0.0131 Å °0.0059 Å °0.0018 Å °0.0013 Å °-0.0078 Å °-0.0051 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 360
2X-RAY DIFFRACTION1B3 - 361
3X-RAY DIFFRACTION1C5 - 360
4X-RAY DIFFRACTION1D3 - 361

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