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

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Basic information

Entry
Database: PDB / ID: 6ohb
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)201,4908
Polymers201,2284
Non-polymers2624
Water3,621201
1
A: Guanine deaminase
C: 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 area4220 Å2
ΔGint-93 kcal/mol
Surface area28580 Å2
MethodPISA
2
B: 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 area3940 Å2
ΔGint-91 kcal/mol
Surface area28610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.479, 137.583, 98.581
Angle α, β, γ (deg.)90.000, 102.161, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPSERSER(chain 'A' and ((resid 62 and (name N or name...AA62 - 8862 - 88
12GLNGLNGLUGLU(chain 'A' and ((resid 62 and (name N or name...AA97 - 11797 - 117
13ARGARGLEULEU(chain 'A' and ((resid 62 and (name N or name...AA120 - 130120 - 130
14ASNASNSERSER(chain 'A' and ((resid 62 and (name N or name...AA133 - 301133 - 301
15TYRTYRGLNGLN(chain 'A' and ((resid 62 and (name N or name...AA304 - 350304 - 350
16ARGARGGLNGLN(chain 'A' and ((resid 62 and (name N or name...AA353 - 399353 - 399
17ASNASNSERSER(chain 'A' and ((resid 62 and (name N or name...AA405 - 424405 - 424
18ARGARGVALVAL(chain 'A' and ((resid 62 and (name N or name...AA427 - 435427 - 435
19ARGARGARGARG(chain 'A' and ((resid 62 and (name N or name...AA438438
21ASPASPSERSER(chain 'B' and ((resid 62 and (name N or name...BB62 - 8862 - 88
22GLNGLNGLUGLU(chain 'B' and ((resid 62 and (name N or name...BB97 - 11797 - 117
23ARGARGLEULEU(chain 'B' and ((resid 62 and (name N or name...BB120 - 130120 - 130
24ASNASNSERSER(chain 'B' and ((resid 62 and (name N or name...BB133 - 301133 - 301
25TYRTYRGLNGLN(chain 'B' and ((resid 62 and (name N or name...BB304 - 350304 - 350
26ARGARGGLNGLN(chain 'B' and ((resid 62 and (name N or name...BB353 - 399353 - 399
27ASNASNSERSER(chain 'B' and ((resid 62 and (name N or name...BB405 - 424405 - 424
28ARGARGVALVAL(chain 'B' and ((resid 62 and (name N or name...BB427 - 435427 - 435
29ARGARGARGARG(chain 'B' and ((resid 62 and (name N or name...BB438438
31ASPASPSERSER(chain 'C' and (resid 62 through 63 or (resid 64...CC62 - 8862 - 88
32GLNGLNGLUGLU(chain 'C' and (resid 62 through 63 or (resid 64...CC97 - 11797 - 117
33ARGARGLEULEU(chain 'C' and (resid 62 through 63 or (resid 64...CC120 - 130120 - 130
34ASNASNSERSER(chain 'C' and (resid 62 through 63 or (resid 64...CC133 - 301133 - 301
35TYRTYRGLNGLN(chain 'C' and (resid 62 through 63 or (resid 64...CC304 - 350304 - 350
36ARGARGGLNGLN(chain 'C' and (resid 62 through 63 or (resid 64...CC353 - 399353 - 399
37ASNASNSERSER(chain 'C' and (resid 62 through 63 or (resid 64...CC405 - 424405 - 424
38ARGARGVALVAL(chain 'C' and (resid 62 through 63 or (resid 64...CC427 - 435427 - 435
39ARGARGARGARG(chain 'C' and (resid 62 through 63 or (resid 64...CC438438
41ASPASPSERSER(chain 'D' and (resid 62 through 63 or (resid 64...DD62 - 8862 - 88
42GLNGLNGLUGLU(chain 'D' and (resid 62 through 63 or (resid 64...DD97 - 11797 - 117
43ARGARGLEULEU(chain 'D' and (resid 62 through 63 or (resid 64...DD120 - 130120 - 130
44ASNASNSERSER(chain 'D' and (resid 62 through 63 or (resid 64...DD133 - 301133 - 301
45TYRTYRGLNGLN(chain 'D' and (resid 62 through 63 or (resid 64...DD304 - 350304 - 350
46ARGARGGLNGLN(chain 'D' and (resid 62 through 63 or (resid 64...DD353 - 399353 - 399
47ASNASNSERSER(chain 'D' and (resid 62 through 63 or (resid 64...DD405 - 424405 - 424
48ARGARGVALVAL(chain 'D' and (resid 62 through 63 or (resid 64...DD427 - 435427 - 435
49ARGARGARGARG(chain 'D' and (resid 62 through 63 or (resid 64...DD438438

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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-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20% Peg3350 100 mM Bis-tris propane pH 7.6 30 mM Citric acid

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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 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.3→55.99 Å / Num. obs: 73766 / % possible obs: 96.6 % / Redundancy: 2.4 % / Biso Wilson estimate: 45.36 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.061 / Net I/σ(I): 8.3
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 0.55 / Num. unique obs: 4626 / CC1/2: 0.731

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OOD

2ood


Resolution: 2.3→55.99 Å / SU ML: 0.299 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8213
RfactorNum. reflection% reflection
Rfree0.2343 3761 5.1 %
Rwork0.1856 --
obs0.188 73766 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.33 Å2
Refinement stepCycle: LAST / Resolution: 2.3→55.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13672 0 4 201 13877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004414040
X-RAY DIFFRACTIONf_angle_d0.795619071
X-RAY DIFFRACTIONf_chiral_restr0.05072093
X-RAY DIFFRACTIONf_plane_restr0.0052448
X-RAY DIFFRACTIONf_dihedral_angle_d4.511410564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.32691530.27152622X-RAY DIFFRACTION97.51
2.33-2.360.3441420.25512617X-RAY DIFFRACTION97.35
2.36-2.390.33971460.25242588X-RAY DIFFRACTION96.61
2.39-2.430.29631400.24492630X-RAY DIFFRACTION97.23
2.43-2.460.33111410.25082588X-RAY DIFFRACTION95.39
2.46-2.50.32171280.2582516X-RAY DIFFRACTION94.87
2.5-2.540.31271280.24772531X-RAY DIFFRACTION93.3
2.54-2.590.32791390.23832646X-RAY DIFFRACTION98.2
2.59-2.630.28261640.23782614X-RAY DIFFRACTION98.58
2.63-2.680.30521310.23752655X-RAY DIFFRACTION98.17
2.68-2.740.29951230.23512691X-RAY DIFFRACTION98.25
2.74-2.80.28591440.23382618X-RAY DIFFRACTION98.36
2.8-2.860.28511360.22022650X-RAY DIFFRACTION97.86
2.86-2.930.3111550.22072598X-RAY DIFFRACTION97.55
2.93-3.010.30231590.22382622X-RAY DIFFRACTION97.31
3.01-3.10.24091490.22022583X-RAY DIFFRACTION96.3
3.1-3.20.27881510.21282588X-RAY DIFFRACTION96.31
3.2-3.320.27511230.21252617X-RAY DIFFRACTION95.67
3.32-3.450.26021250.20792547X-RAY DIFFRACTION94.68
3.45-3.610.24751540.18892451X-RAY DIFFRACTION91.6
3.61-3.80.22751160.182472X-RAY DIFFRACTION90.58
3.8-4.030.2031240.1622620X-RAY DIFFRACTION96.35
4.03-4.350.18921230.15252632X-RAY DIFFRACTION96.6
4.35-4.780.16411490.13322605X-RAY DIFFRACTION96.39
4.78-5.470.1881440.14532599X-RAY DIFFRACTION95.71
5.47-6.90.19161400.16812502X-RAY DIFFRACTION92.31
6.9-56.010.16321340.13912603X-RAY DIFFRACTION93.86

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