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- PDB-6b5x: Beta-Lactamase, unmixed shards crystal form -

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Basic information

Entry
Database: PDB / ID: 6b5x
TitleBeta-Lactamase, unmixed shards crystal form
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-Lactamase / ANTIBIOTIC
Function / homology
Function and homology information


: / : / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / Resolution: 2.45 Å
AuthorsPandey, S.
Funding support United States, 1items
OrganizationGrant numberCountry
United States
CitationJournal: BMC Biol. / Year: 2018
Title: Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography.
Authors: Olmos, J.L. / Pandey, S. / Martin-Garcia, J.M. / Calvey, G. / Katz, A. / Knoska, J. / Kupitz, C. / Hunter, M.S. / Liang, M. / Oberthuer, D. / Yefanov, O. / Wiedorn, M. / Heyman, M. / Holl, M. ...Authors: Olmos, J.L. / Pandey, S. / Martin-Garcia, J.M. / Calvey, G. / Katz, A. / Knoska, J. / Kupitz, C. / Hunter, M.S. / Liang, M. / Oberthuer, D. / Yefanov, O. / Wiedorn, M. / Heyman, M. / Holl, M. / Pande, K. / Barty, A. / Miller, M.D. / Stern, S. / Roy-Chowdhury, S. / Coe, J. / Nagaratnam, N. / Zook, J. / Verburgt, J. / Norwood, T. / Poudyal, I. / Xu, D. / Koglin, J. / Seaberg, M.H. / Zhao, Y. / Bajt, S. / Grant, T. / Mariani, V. / Nelson, G. / Subramanian, G. / Bae, E. / Fromme, R. / Fung, R. / Schwander, P. / Frank, M. / White, T.A. / Weierstall, U. / Zatsepin, N. / Spence, J. / Fromme, P. / Chapman, H.N. / Pollack, L. / Tremblay, L. / Ourmazd, A. / Phillips, G.N. / Schmidt, M.
History
DepositionSep 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9838
Polymers113,6034
Non-polymers3804
Water5,062281
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4962
Polymers28,4011
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4962
Polymers28,4011
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4962
Polymers28,4011
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4962
Polymers28,4011
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.040, 97.190, 110.620
Angle α, β, γ (deg.)90.00, 108.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase / Ambler class A beta-lactamase


Mass: 28400.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: blaC, blaA, Rv2068c, MTCY49.07c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WKD3, beta-lactamase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 3.56 Å3/Da / Density % sol: 65.43 %
Crystal growTemperature: 300 K / Method: microbatch / Details: Ammonium Phosphate

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Sep 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 52485 / % possible obs: 100 % / Redundancy: 1220.89 % / Net I/σ(I): 8.9
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 103.3 % / Mean I/σ(I) obs: 2.4 / CC1/2: 0.411 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementResolution: 2.45→19.979 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 2555 4.88 %
Rwork0.1938 --
obs0.1963 52376 89.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→19.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 20 281 8253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098124
X-RAY DIFFRACTIONf_angle_d1.10111092
X-RAY DIFFRACTIONf_dihedral_angle_d14.64844
X-RAY DIFFRACTIONf_chiral_restr0.0561276
X-RAY DIFFRACTIONf_plane_restr0.0071468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.4970.38561150.32542227X-RAY DIFFRACTION73
2.497-2.54790.3738970.30862293X-RAY DIFFRACTION74
2.5479-2.60320.38541280.29082197X-RAY DIFFRACTION73
2.6032-2.66360.34041250.28582156X-RAY DIFFRACTION71
2.6636-2.73010.36721050.2852292X-RAY DIFFRACTION74
2.7301-2.80370.35831260.27132506X-RAY DIFFRACTION83
2.8037-2.8860.33791550.2622696X-RAY DIFFRACTION88
2.886-2.97880.31011450.23552934X-RAY DIFFRACTION95
2.9788-3.08490.28191540.21523033X-RAY DIFFRACTION99
3.0849-3.20790.25751500.20733057X-RAY DIFFRACTION99
3.2079-3.35330.25761590.19783050X-RAY DIFFRACTION99
3.3533-3.52920.22381620.17993013X-RAY DIFFRACTION99
3.5292-3.74890.20411460.17693055X-RAY DIFFRACTION98
3.7489-4.03620.24631420.17442999X-RAY DIFFRACTION97
4.0362-4.43840.21921530.16023042X-RAY DIFFRACTION98
4.4384-5.07140.19571690.1543055X-RAY DIFFRACTION99
5.0714-6.35510.22451770.1783058X-RAY DIFFRACTION99
6.3551-19.97940.17331470.16153158X-RAY DIFFRACTION99

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