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- PDB-6ni1: Crystal Structure of the Beta Lactamase Class A penP from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 6ni1
TitleCrystal Structure of the Beta Lactamase Class A penP from Bacillus subtilis
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta lactamase class A / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyBeta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID / :
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKim, Y. / Maltseva, N. / Endres, M. / 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 A penP from Bacillus subtilis
Authors: Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,67912
Polymers60,2022
Non-polymers47610
Water5,747319
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2554
Polymers30,1011
Non-polymers1543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4238
Polymers30,1011
Non-polymers3227
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.849, 87.849, 149.853
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Beta-lactamase


Mass: 30101.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Gene: penP, S101441_02191 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Y0WMN3, beta-lactamase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 0.1 M magnesium formate 15 %(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 51645 / % possible obs: 99.9 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 23
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 2.67 / Num. unique obs: 2555 / CC1/2: 0.825 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 3QHY

3qhy


Resolution: 1.9→43.924 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.49
RfactorNum. reflection% reflection
Rfree0.1908 2505 4.86 %
Rwork0.1558 --
obs0.1575 51584 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4146 0 31 319 4496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094275
X-RAY DIFFRACTIONf_angle_d0.9265774
X-RAY DIFFRACTIONf_dihedral_angle_d11.6412603
X-RAY DIFFRACTIONf_chiral_restr0.059667
X-RAY DIFFRACTIONf_plane_restr0.005743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8944-1.93080.23421100.19712466X-RAY DIFFRACTION90
1.9308-1.97020.2371360.18712732X-RAY DIFFRACTION100
1.9702-2.01310.21751530.17312702X-RAY DIFFRACTION100
2.0131-2.05990.21711530.17012750X-RAY DIFFRACTION100
2.0599-2.11140.1721440.15432730X-RAY DIFFRACTION100
2.1114-2.16850.17881450.14832726X-RAY DIFFRACTION100
2.1685-2.23230.18181480.14992728X-RAY DIFFRACTION100
2.2323-2.30440.19851630.14962741X-RAY DIFFRACTION100
2.3044-2.38670.17191030.14942755X-RAY DIFFRACTION100
2.3867-2.48230.19321510.14912738X-RAY DIFFRACTION100
2.4823-2.59520.19281310.15132753X-RAY DIFFRACTION100
2.5952-2.7320.20821370.16212742X-RAY DIFFRACTION100
2.732-2.90320.20781340.1682731X-RAY DIFFRACTION100
2.9032-3.12730.211290.17732762X-RAY DIFFRACTION100
3.1273-3.44190.19921270.16882764X-RAY DIFFRACTION100
3.4419-3.93960.16561540.15532746X-RAY DIFFRACTION100
3.9396-4.96240.18071300.13482760X-RAY DIFFRACTION100
4.9624-43.93630.18891570.14982753X-RAY DIFFRACTION99
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)
13.7654-0.08940.43944.2884-0.7874.00940.0592-1.1213-0.49141.1066-0.00280.1354-0.1999-0.2728-0.02190.467-0.02570.02020.62070.02140.36-16.296833.0272-29.2417
22.46490.29170.73981.51670.16371.5295-0.03670.2958-0.1402-0.22120.042-0.16740.01780.26060.020.23440.0068-0.00330.2669-0.0250.2371-2.573329.9789-54.083
32.82860.41280.93960.83920.31170.8871-0.1897-0.08370.47140.027-0.03630.0908-0.2042-0.1730.22130.2540.0248-0.04790.2674-0.02840.3076-11.051236.1548-44.5522
43.5428-0.81041.8323.5433-1.54087.5078-0.1777-0.63080.27590.56310-0.0651-0.32830.21510.19530.32030.0223-0.02960.3808-0.07940.3023-8.634739.1321-35.5716
51.98810.34690.15022.45530.27161.4464-0.12020.43790.1038-0.66440.0725-0.1055-0.21820.08730.00660.3584-0.03060.01220.28090.00370.2608-22.446224.8558-16.6516
61.34080.37090.05972.88420.04312.55750.1177-0.4389-0.09080.5549-0.06860.01580.1866-0.0858-0.00770.3394-0.04-0.01960.39310.02680.3003-28.939310.051714.3506
71.10340.25360.39951.0838-0.09741.41320.0503-0.1202-0.08480.0379-0.0402-0.08390.0488-0.1123-0.01420.2010.0008-0.00290.2323-0.0190.2285-26.022316.16120.0661
82.4717-0.1804-0.0544.07062.05385.5473-0.04630.30350.166-0.5201-0.06280.2066-0.0893-0.24290.07550.29210.0076-0.04020.27820.00690.2753-32.833124.7316-14.4385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 38 through 60 )
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 267 )
3X-RAY DIFFRACTION3chain 'A' and (resid 268 through 290 )
4X-RAY DIFFRACTION4chain 'A' and (resid 291 through 306 )
5X-RAY DIFFRACTION5chain 'B' and (resid 38 through 87 )
6X-RAY DIFFRACTION6chain 'B' and (resid 88 through 135 )
7X-RAY DIFFRACTION7chain 'B' and (resid 136 through 290 )
8X-RAY DIFFRACTION8chain 'B' and (resid 291 through 306 )

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