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- PDB-6ohc: E. coli Guanine Deaminase -

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Basic information

Entry
Database: PDB / ID: 6ohc
TitleE. coli Guanine Deaminase
ComponentsGuanine deaminase
KeywordsHYDROLASE / amidohydrolase guanine deaminase purine metabolism
Function / homology
Function and homology information


ammeline aminohydrolase activity / guanine deaminase / guanine deaminase activity / guanine catabolic process / guanine metabolic process / zinc ion binding / cytosol
Similarity search - Function
Guanine deaminase / : / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShek, R.S. / French, J.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124898 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103403 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structural Determinants for Substrate Selectivity in Guanine Deaminase Enzymes of the Amidohydrolase Superfamily.
Authors: Shek, R. / Hilaire, T. / Sim, J. / French, J.B.
History
DepositionApr 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanine deaminase
B: Guanine deaminase
C: Guanine deaminase
D: Guanine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,67410
Polymers201,2284
Non-polymers4466
Water6,521362
1
A: Guanine deaminase
B: Guanine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,9296
Polymers100,6142
Non-polymers3154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-90 kcal/mol
Surface area29240 Å2
MethodPISA
2
C: Guanine deaminase
D: Guanine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7454
Polymers100,6142
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-92 kcal/mol
Surface area29630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.628, 80.588, 101.427
Angle α, β, γ (deg.)104.800, 105.720, 105.830
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISAA6 - 4396 - 439
21HISHISBB6 - 4396 - 439
12HISHISAA6 - 4396 - 439
22HISHISCC6 - 4396 - 439
13GLUGLUAA5 - 4395 - 439
23GLUGLUDD5 - 4395 - 439
14HISHISBB6 - 4396 - 439
24HISHISCC6 - 4396 - 439
15HISHISBB6 - 4396 - 439
25HISHISDD6 - 4396 - 439
16HISHISCC6 - 4396 - 439
26HISHISDD6 - 4396 - 439

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Guanine deaminase / Guanine aminase / Guanine aminohydrolase / GAH


Mass: 50307.074 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: guaD, ygfP, b2883, JW5466 / Production host: Escherichia coli (E. coli) / References: UniProt: P76641, guanine deaminase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Hepes pH 7.5 10% Peg 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9198 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.3→48.91 Å / Num. obs: 79427 / % possible obs: 98 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.039 / Rrim(I) all: 0.097 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 5.9 % / Num. unique obs: 4380 / CC1/2: 0.756 / Rpim(I) all: 0.504 / % possible all: 96

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OOD

2ood


Resolution: 2.3→48.91 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 20.444 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.388 / ESU R Free: 0.257
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 3958 5 %RANDOM
Rwork0.2086 ---
obs0.2111 75330 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 143.45 Å2 / Biso mean: 56.557 Å2 / Biso min: 27.71 Å2
Baniso -1Baniso -2Baniso -3
1--3.85 Å21.14 Å2-0.86 Å2
2--1.14 Å2-0.02 Å2
3---1.67 Å2
Refinement stepCycle: final / Resolution: 2.3→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13059 0 16 362 13437
Biso mean--59.94 50.73 -
Num. residues----1710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01313413
X-RAY DIFFRACTIONr_bond_other_d0.0020.01711671
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.64318264
X-RAY DIFFRACTIONr_angle_other_deg1.3551.57326869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22451704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9722.146671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.177151985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4261573
X-RAY DIFFRACTIONr_chiral_restr0.0730.21763
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215375
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022973
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A141590.09
12B141590.09
21A125260.07
22C125260.07
31A131540.09
32D131540.09
41B123790.09
42C123790.09
51B131480.09
52D131480.09
61C120530.09
62D120530.09
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 278 -
Rwork0.348 5412 -
all-5690 -
obs--95.74 %
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)
10.4886-0.2743-0.11120.37340.18130.20580.0265-0.1343-0.1232-0.13720.00030.1201-0.04080.0289-0.02680.32350.0048-0.03960.2238-0.00990.428229.2321-106.34227.5911
20.6154-0.25240.23710.6332-0.17080.1070.0509-0.05660.1031-0.1511-0.066-0.1160.0172-0.01980.01510.37540.01970.03040.2028-0.02470.390447.6077-74.761819.8086
31.4453-0.4298-0.22540.3155-0.13620.7542-0.0443-0.3961-0.01310.1434-0.0121-0.0276-0.527-0.07590.05640.4290.094-0.03250.5956-0.16020.114147.5181-69.848961.1686
41.455-0.50080.13460.19960.00930.4393-0.0441-0.414-0.3824-0.04230.12050.0994-0.1089-0.017-0.07640.15950.0123-0.01280.52020.14380.356653.1489-106.070261.0125
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 439
2X-RAY DIFFRACTION2B6 - 439
3X-RAY DIFFRACTION3C6 - 439
4X-RAY DIFFRACTION4D5 - 439

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