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- PDB-1hl7: Gamma lactamase from an Aureobacterium species in complex with 3a... -

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Basic information

Entry
Database: PDB / ID: 1hl7
TitleGamma lactamase from an Aureobacterium species in complex with 3a,4,7,7a-tetrahydro-benzo [1,3] dioxol-2-one
ComponentsGAMMA LACTAMASE
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE / CO-FACTOR FREE HALOPEROXIDASE / TETRAHEDRAL INTERMEDIATE
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
3A,4,7,7A-TETRAHYDRO-BENZO [1,3] DIOXOL-2-ONE / Co-factor free haloperoxidase
Similarity search - Component
Biological speciesMICROBACTERIUM SP. (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 14, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)62,0414
Polymers61,7572
Non-polymers2842
Water12,268681
1
A: GAMMA LACTAMASE
hetero molecules

A: GAMMA LACTAMASE
hetero molecules

A: GAMMA LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0616
Polymers92,6353
Non-polymers4263
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)93,0616
Polymers92,6353
Non-polymers4263
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)240.592, 240.592, 240.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.32744, 0.77849, -0.53548), (0.53932, 0.31134, 0.78243), (0.77583, -0.545, -0.31791)
Vector: 99.5468, -112.77448, -8.95121)

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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 SP. (bacteria) / Description: CHIROTECH CULTURE COLLECTION / Plasmid: PTRC99 / Production host: ESCHERICHIA COLI DH5[ALPHA] (bacteria) / References: UniProt: Q8GJP7
#2: Chemical ChemComp-BD1 / 3A,4,7,7A-TETRAHYDRO-BENZO [1,3] DIOXOL-2-ONE


Mass: 142.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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

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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: 118797 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 28.18
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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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: 0.981 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.06
RfactorNum. reflection% reflectionSelection details
Rfree0.165 2388 2 %RANDOM
Rwork0.151 ---
obs-118797 100 %-
Displacement parametersBiso mean: 15.6 Å2
Refinement stepCycle: LAST / Resolution: 1.73→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 20 681 5077

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