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- PDB-5e43: Crystal Structure of Beta-lactamase Sros_5706 from Streptosporang... -

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Basic information

Entry
Database: PDB / ID: 5.0E+43
TitleCrystal Structure of Beta-lactamase Sros_5706 from Streptosporangium roseum
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / 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
ACETATE ION / NITRATE ION / Beta-lactamase
Similarity search - Component
Biological speciesStreptosporangium roseum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7095 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 Sros_5706 from Streptosporangium roseum
Authors: Kim, Y. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Joachimiak, A.
History
DepositionOct 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,83220
Polymers31,7041
Non-polymers1,12819
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-2 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.845, 92.932, 85.629
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-301-

NO3

21A-301-

NO3

31A-309-

NO3

41A-309-

NO3

51A-486-

HOH

61A-497-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 31704.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptosporangium roseum (strain ATCC 12428 / DSM 43021 / JCM 3005 / NI 9100) (bacteria)
Strain: ATCC 12428 / DSM 43021 / JCM 3005 / NI 9100 / Gene: Sros_5706 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold / References: UniProt: D2ARB3, beta-lactamase
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 6.0 M Ammonium nitrate, 0.1 M, Sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 32159 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rsym value: 0.149 / Net I/σ(I): 17.12
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 1.89 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2104: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.7095→29.146 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.06 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1871 1625 5.06 %Random selection
Rwork0.1593 30494 --
obs0.1607 32119 98.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7095→29.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 76 155 2258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092160
X-RAY DIFFRACTIONf_angle_d0.9732915
X-RAY DIFFRACTIONf_dihedral_angle_d15.0761275
X-RAY DIFFRACTIONf_chiral_restr0.062330
X-RAY DIFFRACTIONf_plane_restr0.006388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7095-1.75980.3021140.26682084X-RAY DIFFRACTION83
1.7598-1.81660.28041490.22292539X-RAY DIFFRACTION100
1.8166-1.88150.18671270.18342561X-RAY DIFFRACTION100
1.8815-1.95680.19011420.15892537X-RAY DIFFRACTION100
1.9568-2.04590.19931320.15352578X-RAY DIFFRACTION100
2.0459-2.15370.18351350.14552559X-RAY DIFFRACTION100
2.1537-2.28860.18521250.14342573X-RAY DIFFRACTION100
2.2886-2.46520.17641540.14772553X-RAY DIFFRACTION100
2.4652-2.71310.20481230.1582606X-RAY DIFFRACTION100
2.7131-3.10540.19061190.16062616X-RAY DIFFRACTION100
3.1054-3.91090.1711430.14952612X-RAY DIFFRACTION100
3.9109-29.14970.171620.15812676X-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)
12.02871.69810.61327.02860.14795.9821-0.02380.3275-0.5268-0.534-0.0320.26510.3692-0.31920.09240.2937-0.0042-0.01790.2198-0.03510.220932.07333.329526.7689
20.83310.04890.50091.2820.59241.08120.03050.0533-0.0614-0.0185-0.07550.06940.0514-0.07090.04190.1579-0.00360.01090.16460.010.149328.607212.675943.5136
32.0410.33240.44031.1670.4511.6642-0.06040.15390.1476-0.09180.0764-0.0455-0.17010.1035-0.02120.186-0.00450.00290.15650.01530.165638.209832.079554.3458
40.78120.09670.34141.0570.56831.68080.0020.01770.0010.0232-0.00480.0217-0.0119-0.04360.0040.15580.00190.00890.1763-0.00350.162431.179717.70848.0018
52.47950.32640.26712.00420.39772.0489-0.04120.1032-0.0317-0.13190.0134-0.1113-0.06610.08950.03870.18490.0140.00580.1820.00590.148832.118915.466634.183
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 86 )
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 132 )
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 230 )
5X-RAY DIFFRACTION5chain 'A' and (resid 231 through 294 )

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