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- PDB-4gyr: Granulibacter bethesdensis allophanate hydrolase apo -

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Basic information

Entry
Database: PDB / ID: 4gyr
TitleGranulibacter bethesdensis allophanate hydrolase apo
ComponentsAllophanate hydrolase
KeywordsHYDROLASE / Amidase signature family enzyme
Function / homology
Function and homology information


allophanate hydrolase activity / allophanate hydrolase
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1700 / Allophanate hydrolase / : / Allophanate hydrolase C-terminal domain / Amidase / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1700 / Allophanate hydrolase / : / Allophanate hydrolase C-terminal domain / Amidase / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Allophanate hydrolase
Similarity search - Component
Biological speciesGranulibacter bethesdensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLin, Y. / St Maurice, M.
CitationJournal: Biochemistry / Year: 2013
Title: The Structure of Allophanate Hydrolase from Granulibacter bethesdensis Provides Insights into Substrate Specificity in the Amidase Signature Family.
Authors: Lin, Y. / St Maurice, M.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Allophanate hydrolase
B: Allophanate hydrolase


Theoretical massNumber of molelcules
Total (without water)133,0742
Polymers133,0742
Non-polymers00
Water2,090116
1
B: Allophanate hydrolase

A: Allophanate hydrolase


Theoretical massNumber of molelcules
Total (without water)133,0742
Polymers133,0742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x-y,x+1,z+1/61
2
A: Allophanate hydrolase


Theoretical massNumber of molelcules
Total (without water)66,5371
Polymers66,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Allophanate hydrolase


Theoretical massNumber of molelcules
Total (without water)66,5371
Polymers66,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.094, 78.094, 397.543
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 2:46 or resseq 48:346 or resseq 348:462 )
211chain B and (resseq 2:46 or resseq 48:346 or resseq 348:462 )
DetailsThe biological unit consists of chain A from Sym ID 6_565 and chain B from the identity matrix (Sym ID 1_555)

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Components

#1: Protein Allophanate hydrolase


Mass: 66537.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Granulibacter bethesdensis (bacteria) / Strain: ATCC BAA-1260 / CGDNIH1 / Gene: GbCGDNIH1_1744 / Plasmid: pET28a-(HIS)8-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: Q0BRB0, allophanate hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24%(w/v)PEG4000,50mM MgCl2,100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 33600 / Num. obs: 33519 / % possible obs: 99.9 % / Redundancy: 9 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 20.8
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 18.1 / Num. unique all: 1634 / % possible all: 100

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Processing

Software
NameVersionClassification
MC-2diffractometer software from EMBLdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GYS

4gys


Resolution: 2.8→40.045 Å / SU ML: 0.88 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 30.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3068 2026 6.05 %RANDOM
Rwork0.2562 ---
obs0.2594 33489 99.87 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.529 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.9635 Å2-0 Å2-0 Å2
2--4.9635 Å20 Å2
3----9.2344 Å2
Refinement stepCycle: LAST / Resolution: 2.8→40.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6806 0 0 116 6922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056958
X-RAY DIFFRACTIONf_angle_d0.9069507
X-RAY DIFFRACTIONf_dihedral_angle_d17.3862473
X-RAY DIFFRACTIONf_chiral_restr0.0591107
X-RAY DIFFRACTIONf_plane_restr0.0041258
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3370X-RAY DIFFRACTIONPOSITIONAL
12B3370X-RAY DIFFRACTIONPOSITIONAL0.053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8003-2.87030.36261450.29642234X-RAY DIFFRACTION100
2.8703-2.94780.35641450.2992233X-RAY DIFFRACTION100
2.9478-3.03460.35231440.28322251X-RAY DIFFRACTION100
3.0346-3.13250.37421430.28562274X-RAY DIFFRACTION100
3.1325-3.24440.34571430.28222237X-RAY DIFFRACTION100
3.2444-3.37420.33051480.2672246X-RAY DIFFRACTION100
3.3742-3.52770.31051450.27722231X-RAY DIFFRACTION100
3.5277-3.71360.35611470.25962267X-RAY DIFFRACTION100
3.7136-3.9460.31481380.2432232X-RAY DIFFRACTION100
3.946-4.25040.29451510.22642244X-RAY DIFFRACTION100
4.2504-4.67760.24971450.21312247X-RAY DIFFRACTION100
4.6776-5.3530.29071420.22452252X-RAY DIFFRACTION100
5.353-6.73910.30441440.27832252X-RAY DIFFRACTION100
6.7391-40.04940.24021460.25862263X-RAY DIFFRACTION99

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