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- PDB-2xh9: Structural and mechanistic studies on a cephalosporin esterase fr... -

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Basic information

Entry
Database: PDB / ID: 2xh9
TitleStructural and mechanistic studies on a cephalosporin esterase from the clavulanic acid biosynthesis pathway
ComponentsORF12
KeywordsHYDROLASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / response to antibiotic
Similarity search - Function
ORF12 helical bundle domain-like / Nuclear Transport Factor 2; Chain: A, - #280 / ORF 12 gene product, N-terminal / ORF 12 gene product N-terminal / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Nuclear Transport Factor 2; Chain: A, / Helicase, Ruva Protein; domain 3 / Beta-lactamase ...ORF12 helical bundle domain-like / Nuclear Transport Factor 2; Chain: A, - #280 / ORF 12 gene product, N-terminal / ORF 12 gene product N-terminal / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Nuclear Transport Factor 2; Chain: A, / Helicase, Ruva Protein; domain 3 / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Roll / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-J01 / Beta-lactamase / Uncharacterized protein
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsIqbal, A. / Valegard, K. / Kershaw, N.J. / Ivison, D. / Genereux, C. / Dubus, A. / Andersson, I. / Schofield, C.J.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: Structural and mechanistic studies of the orf12 gene product from the clavulanic acid biosynthesis pathway.
Authors: Valegard, K. / Iqbal, A. / Kershaw, N.J. / Ivison, D. / Genereux, C. / Dubus, A. / Blikstad, C. / Demetriades, M. / Hopkinson, R.J. / Lloyd, A.J. / Roper, D.I. / Schofield, C.J. / Andersson, I. / McDonough, M.A.
History
DepositionJun 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references / Version format compliance
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF12
B: ORF12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5686
Polymers99,7712
Non-polymers7974
Water11,512639
1
A: ORF12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2843
Polymers49,8861
Non-polymers3982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ORF12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2843
Polymers49,8861
Non-polymers3982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.514, 100.895, 81.355
Angle α, β, γ (deg.)90.00, 93.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ORF12


Mass: 49885.594 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83Z62, UniProt: Q8KRB7*PLUS
#2: Chemical
ChemComp-J01 / (2R,3Z,5R)-3-(2-HYDROXYETHYLIDENE)-7-OXO-4-OXA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID / CLAVULANIC ACID


Mass: 199.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H9NO5 / Comment: antibiotic, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 378 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 378 TO ALA

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 8
Details: 13%(W/V) PEG4000,0.1M NAAC,0.1M NACL,10%(W/V) GLYCEROL,0.1M TRIS/HCL PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→81.1 Å / Num. obs: 89909 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.25 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XEP

2xep


Resolution: 1.8→81.11 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.375 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22821 4497 5 %RANDOM
Rwork0.19706 ---
obs0.19862 85397 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.061 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å2-0.5 Å2
2--0.7 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→81.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6538 0 56 639 7233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216750
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.9749193
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4765846
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.89522.708288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.894151090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8871564
X-RAY DIFFRACTIONr_chiral_restr0.1050.21046
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025128
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.23143
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24623
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2576
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8531.54314
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34126771
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.22632761
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.54.52412
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 324 -
Rwork0.229 5680 -
obs--88.44 %

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