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- PDB-1hkh: unligated gamma lactamase from an Aureobacterium species -

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Basic information

Entry
Database: PDB / ID: 1hkh
Titleunligated gamma lactamase from an Aureobacterium species
ComponentsGAMMA LACTAMASE
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE / CO-FACTOR FREE HALOPEROXIDASE
Function / homology
Function and homology information


peroxidase activity
Similarity search - Function
: / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Co-factor free haloperoxidase
Similarity search - Component
Biological speciesMICROBACTERIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsLine, K. / Isupov, M.N. / Littlechild, J.A.
CitationJournal: J. Mol. Biol. / Year: 2004
Title: The crystal structure of a (-) gamma-lactamase from an Aureobacterium species reveals a tetrahedral intermediate in the active site.
Authors: Line, K. / Isupov, M.N. / Littlechild, J.A.
History
DepositionMar 10, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_special_symmetry / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GAMMA LACTAMASE
B: GAMMA LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9494
Polymers61,7572
Non-polymers1922
Water15,187843
1
A: GAMMA LACTAMASE
hetero molecules

A: GAMMA LACTAMASE
hetero molecules

A: GAMMA LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9236
Polymers92,6353
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_555z,-x+1/2,-y+1/21
crystal symmetry operation48_555-y+1/2,-z+1/2,x1
MethodPQS
2
B: GAMMA LACTAMASE
hetero molecules

B: GAMMA LACTAMASE
hetero molecules

B: GAMMA LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9236
Polymers92,6353
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation34_555-y+1/2,z,-x+1/21
crystal symmetry operation43_555-z+1/2,-x+1/2,y1
MethodPQS
Unit cell
Length a, b, c (Å)240.874, 240.874, 240.874
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11B-2003-

HOH

21B-2006-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.32713, 0.77924, -0.53457), (0.53979, 0.31023, 0.78255), (0.77564, -0.54455, -0.31914)
Vector: 99.61824, -112.95067, -8.86623)

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Components

#1: Protein GAMMA LACTAMASE / CO-FACTOR FREE HALOPEROXIDASE (BY IDENTITY)


Mass: 30878.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MICROBACTERIUM (bacteria) / Description: CHIROTECH CULTURE COLLECTION / Plasmid: PTRC99 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q8GJP7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 843 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNAMED CO-FACTOR FREE HALOPEROXIDASE DUE TO HIGH SEQUENCE ID

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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: 4.72 Å3/Da / Density % sol: 73.73 %
Crystal growpH: 8 / Details: pH 8.00
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMsodium phosphate1droppH7.5
2100 %satammonium sulfate1drop
310 mg/mlprotein1drop
458 %satammonium sulfate1reservoir
550 mMTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8482
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8482 Å / Relative weight: 1
ReflectionResolution: 1.73→11 Å / Num. obs: 119247 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 24.76
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 11 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.23 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.73 Å / Lowest resolution: 11 Å / % possible obs: 100 % / Redundancy: 11.39 % / Rmerge(I) obs: 0.108
Reflection shell
*PLUS
Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.2

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BRO

1bro


Resolution: 1.73→11 Å / SU B: 1.055 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1582 2400 2 %RANDOM
Rwork0.1443 ---
obs-119247 100 %-
Displacement parametersBiso mean: 16.1 Å2
Refinement stepCycle: LAST / Resolution: 1.73→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 10 843 5229
Refinement
*PLUS
Rfactor Rfree: 0.158 / Rfactor Rwork: 0.144
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONbond_d0.0130.021
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.3471.938

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