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- PDB-6nhs: Crystal Structure of the Beta Lactamase Class D YbXI from Nostoc -

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Basic information

Entry
Database: PDB / ID: 6nhs
TitleCrystal Structure of the Beta Lactamase Class D YbXI from Nostoc
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta lactamase class D / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


penicillin binding / cell wall organization
Similarity search - Function
: / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKim, Y. / Tesar, C. / 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 YbXI from Nostoc
Authors: Kim, Y. / Tesar, C. / Endres, M. / Babnigg, G. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,68613
Polymers30,1011
Non-polymers58512
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-15 kcal/mol
Surface area10980 Å2
2
A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,74552
Polymers120,4064
Non-polymers2,33948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_554y,x,-z-1/31
crystal symmetry operation10_664-y+1,-x+1,-z-1/31
Buried area10190 Å2
ΔGint-89 kcal/mol
Surface area39260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.502, 116.502, 74.702
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-301-

CL

21A-416-

HOH

31A-478-

HOH

41A-498-

HOH

51A-522-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 30101.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: all2480 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YU74
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.05M Bis-Tris pH 6.5, 45%(v/v) PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 20709 / % possible obs: 99.5 % / Redundancy: 23.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 45.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 23.8 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1000 / CC1/2: 0.895 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2→38.134 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.49
RfactorNum. reflection% reflection
Rfree0.2015 990 4.79 %
Rwork0.1631 --
obs0.1649 20664 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.9 Å2
Refinement stepCycle: LAST / Resolution: 2→38.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 34 124 2124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052073
X-RAY DIFFRACTIONf_angle_d0.672796
X-RAY DIFFRACTIONf_dihedral_angle_d15.2721225
X-RAY DIFFRACTIONf_chiral_restr0.046297
X-RAY DIFFRACTIONf_plane_restr0.004366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9967-2.1020.21121290.18662717X-RAY DIFFRACTION98
2.102-2.23370.2141480.162746X-RAY DIFFRACTION99
2.2337-2.40610.21391440.16812752X-RAY DIFFRACTION99
2.4061-2.64820.19421430.16922781X-RAY DIFFRACTION99
2.6482-3.03130.20711340.16772808X-RAY DIFFRACTION99
3.0313-3.81850.18341510.162848X-RAY DIFFRACTION100
3.8185-38.14120.20951410.1583022X-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)
12.091-0.1641-0.98341.58870.87182.66480.03960.027-0.6264-0.1950.19490.370.9202-0.1707-0.12030.6434-0.0846-0.27390.36570.13250.568725.24127.0927-2.9959
20.7048-0.11680.32681.7075-0.94321.21180.0782-0.1523-0.1032-0.0282-0.0476-0.13240.06950.09170.01620.2686-0.0627-0.05640.25430.05490.254335.051231.3599-2.608
31.1229-0.61570.20321.7791-0.07640.83770.0059-0.4077-0.32890.17980.17570.21990.1395-0.2369-0.15810.283-0.0569-0.05760.33440.11080.254126.277628.8186.2711
44.69942.15640.40261.76821.19561.34670.3311-0.1222-0.2509-0.3108-0.10530.35410.1906-0.3031-0.13480.3843-0.0788-0.20930.29930.12770.369616.471226.1774-7.2501
53.1745-0.0760.51050.58290.53981.20880.125-0.10990.0092-0.44420.00060.18140.1321-0.0246-0.07170.4028-0.0506-0.150.28540.1280.329125.141222.9755-6.7741
62.8125-0.7214-0.17470.33850.143.61640.22770.34960.16720.02030.16180.1284-0.19760.0838-0.33460.46940.0337-0.00990.43890.04580.509344.732816.2667-8.0218
71.61120.5420.38371.1236-0.34580.97360.0104-0.08340.1141-0.36660.1810.28070.2469-0.1218-0.08110.3452-0.0728-0.14350.2820.12650.354225.780320.0538-3.0227
83.0485-0.1847-0.23171.9002-0.36271.9377-0.1083-0.1984-0.4223-0.18170.24850.2040.5099-0.226-0.22090.3863-0.0914-0.17140.29110.10.380725.371415.936-2.4819
92.70910.37930.70191.6884-0.08460.20290.11090.5088-0.3185-0.81380.13820.29950.5038-0.1958-0.15850.6229-0.1064-0.28550.33030.12760.477623.211513.11-9.2269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 180 )
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 212 )
4X-RAY DIFFRACTION4chain 'A' and (resid 213 through 221 )
5X-RAY DIFFRACTION5chain 'A' and (resid 222 through 231 )
6X-RAY DIFFRACTION6chain 'A' and (resid 232 through 236 )
7X-RAY DIFFRACTION7chain 'A' and (resid 237 through 247 )
8X-RAY DIFFRACTION8chain 'A' and (resid 248 through 262 )
9X-RAY DIFFRACTION9chain 'A' and (resid 263 through 283 )

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