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- PDB-7k3m: Crystal Structure of the Beta Lactamase Class D from Chitinophaga... -

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Basic information

Entry
Database: PDB / ID: 7k3m
TitleCrystal Structure of the Beta Lactamase Class D from Chitinophaga pinensis by Serial Crystallography
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta lactamase class D / serial crystallography / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyPenicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / penicillin binding / Beta-lactamase/transpeptidase-like / beta-lactamase activity / beta-lactamase / Beta-lactamase
Function and homology information
Biological speciesChitinophaga pinensis DSM 2588 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, Y. / Sherrell, D.A. / Johnson, J. / Lavens, A. / Maltseva, N. / Endres, M. / Babnigg, G. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Beta Lactamase Class D from Chitinophaga pinensis by Serial Crystallography
Authors: Kim, Y. / Sherrell, D.A. / Johnson, J. / Lavens, A. / Maltseva, N. / Endres, M. / Babnigg, G. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Dec 23, 2020Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)29,8801
Polymers29,8801
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.413, 69.347, 70.035
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Beta-lactamase


Mass: 29880.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chitinophaga pinensis DSM 2588 (bacteria)
Gene: Cpin_0907 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: C7PL61, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.01 Å3/Da / Density % sol: 38.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Bis-Tris propane pH 9.0, 8 %(w/v) PEG20000

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→49.28 Å / Num. obs: 23276 / % possible obs: 99.99 % / Redundancy: 79.11 % / CC1/2: 0.97 / Rmerge(I) obs: 0.67 / Net I/σ(I): 2.81
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 0.76 / Num. unique obs: 1134 / CC1/2: 0.73 / % possible all: 99.8
Serial crystallography sample deliveryDescription: Nylon Mesh / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: 60um Nylon mesh / Motion control: PMAC EPICS / Sample holding: ALEX mesh-holder / Support base: SmarAct XYZ stage
Serial crystallography data reductionFrame hits: 36400 / Frames indexed: 8424 / Frames total: 36400 / Lattices indexed: 7261

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
CRISpydata collection
DIALSdata reduction
PRIMEdata scaling
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The crystal structure of the same protein in the complex with avibactam which will be deposited

Resolution: 1.8→49.28 Å / Cross valid method: FREE R-VALUE / σ(F): 1.23 / Phase error: 24.2283
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2243 1107 4.83 %
Rwork0.1775 21833 -
obs0.1829 22940 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.62 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 0 131 2160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272083
X-RAY DIFFRACTIONf_angle_d0.58022811
X-RAY DIFFRACTIONf_chiral_restr0.0453294
X-RAY DIFFRACTIONf_plane_restr0.0038358
X-RAY DIFFRACTIONf_dihedral_angle_d20.5763774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.22531350.21722667X-RAY DIFFRACTION95.11
1.88-1.980.19371150.20232721X-RAY DIFFRACTION95.94
1.98-2.110.23231280.18172686X-RAY DIFFRACTION95.45
2.11-2.270.22211530.17232674X-RAY DIFFRACTION94.59
2.27-2.50.26141420.17372719X-RAY DIFFRACTION95.04
2.5-2.860.22651350.17852724X-RAY DIFFRACTION95.28
2.86-3.60.23651240.17362778X-RAY DIFFRACTION95.73
3.6-49.280.21991670.17562872X-RAY DIFFRACTION94.5
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.311287970720.122198526283-0.06082248281790.122078900620.02123824668690.22893643935-0.01069929547220.03265429917660.0154105075422-0.03534711309680.002601046793010.0269233997131-0.0203986034618-0.06790644559710.003635752941430.05731084259470.00529060879733-0.00655924270790.1665397187680.006145853609370.0298067402415-4.136357576062.98733448697-12.7526965557
20.109862034789-0.0536105043152-0.01180733608590.203896953770.05648141693080.37398642985-0.00652679466458-0.00718783952278-0.002445405836620.00864657937920.005063931884690.000388859972290.0276702423582-0.0016356493092-0.01024054430650.04630840932850.0150628131292-0.0006080513713970.186389299566-0.002736373517150.029267803885116.8032911183-0.0339526550471-6.59141313366
30.1520938709860.07323167240740.06656265249340.2306251847560.03371613332070.287301576034-0.00879310334448-0.00165064357537-0.0005859332708840.003732908847310.0066338732648-0.00557232690586-0.003904716456830.013598260333-0.01067841374980.05170902096280.0101219108358-0.004823025783950.182762607628-0.005410756599750.02766183737235.46581082385-0.709480991788-17.7553837413
40.4489465965130.0918290250105-0.4124800127070.714595546279-0.07417955427111.91604124718-0.0108098409626-0.0267960110546-0.02440184127370.0326267807389-0.0220461366595-0.002610151342460.1269951534750.02691809429750.03184126832380.05940676621330.005671985388430.009498846848020.1518098914020.008199279017130.0346085355222-5.69281581667-6.39276611306-13.8824808893
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 23 through 81 )23 - 811 - 59
22chain 'A' and (resid 82 through 162 )82 - 16260 - 140
33chain 'A' and (resid 163 through 225 )163 - 225141 - 203
44chain 'A' and (resid 226 through 267 )226 - 267204 - 245

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