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- PDB-7ej3: UTP cyclohydrolase -

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Basic information

Entry
Database: PDB / ID: 7ej3
TitleUTP cyclohydrolase
ComponentsGTP cyclohydrolase II
KeywordsHYDROLASE / UTP / URCA / LYASE
Function / homology
Function and homology information


GTP cyclohydrolase II activity / riboflavin biosynthetic process / GTP binding
Similarity search - Function
GTP cyclohydrolase N-terminal / GTP cyclohydrolase N terminal / GTP cyclohydrolase II, RibA / GTP cyclohydrolase II / GTP cyclohydrolase II superfamily / GTP cyclohydrolase II
Similarity search - Domain/homology
DIPHOSPHATE / GLYCINE / GTP cyclohydrolase II
Similarity search - Component
Biological speciesRhodococcus wratislaviensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsZhang, H. / Zhang, Y. / Yuchi, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31870049 China
CitationJournal: Acs Catalysis / Year: 2021
Title: Structural and biochemical investigation of UTP cyclohydrolase
Authors: Zhang, H. / Wei, Y. / Lin, L. / Liu, J. / Chu, R. / Cao, P. / Ang, E.L. / Zhao, H. / Yuchi, Z. / Zhang, Y.
History
DepositionApr 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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: GTP cyclohydrolase II
B: GTP cyclohydrolase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4377
Polymers90,8832
Non-polymers5545
Water20,5731142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-133 kcal/mol
Surface area27060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.152, 115.152, 283.489
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1453-

HOH

21B-857-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 27 through 52 or (resid 53...

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
11GLYGLYLEULEUchain AAA27 - 42325 - 421
21GLYGLYASNASN(chain B and (resid 27 through 52 or (resid 53...BB27 - 5225 - 50
22ARGARGALAALA(chain B and (resid 27 through 52 or (resid 53...BB53 - 5451 - 52
23HISHISASPASP(chain B and (resid 27 through 52 or (resid 53...BB24 - 42422 - 422
24HISHISASPASP(chain B and (resid 27 through 52 or (resid 53...BB24 - 42422 - 422
25HISHISASPASP(chain B and (resid 27 through 52 or (resid 53...BB24 - 42422 - 422
26HISHISASPASP(chain B and (resid 27 through 52 or (resid 53...BB24 - 42422 - 422

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Components

#1: Protein GTP cyclohydrolase II


Mass: 45441.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus wratislaviensis (bacteria) / Gene: C8E05_0284 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3D9R4E8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 15% w/v PEG 8000, 0.5 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9715 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9715 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 146135 / % possible obs: 100 % / Redundancy: 18.5 % / Biso Wilson estimate: 16.39 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.028 / Rrim(I) all: 0.119 / Χ2: 0.69 / Net I/σ(I): 4.1 / Num. measured all: 2709459
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.6319.21.08971730.8550.2541.1180.435100
1.63-1.6619.10.96171600.8760.2240.9870.443100
1.66-1.6919.10.83672160.9020.1950.8580.452100
1.69-1.7218.80.72571970.930.1710.7460.457100
1.72-1.7618.50.62772110.9430.1490.6440.462100
1.76-1.818.10.51972310.9630.1250.5340.48100
1.8-1.8517.20.41871870.9690.1030.430.501100
1.85-1.9180.36372190.9790.0880.3740.518100
1.9-1.9519.40.30472740.9860.070.3120.544100
1.95-2.0219.30.26172280.9880.0610.2680.587100
2.02-2.0919.20.21172520.9920.0490.2160.654100
2.09-2.17190.18472830.9930.0430.1890.715100
2.17-2.2718.30.15472560.9950.0370.1580.806100
2.27-2.3917.20.13673050.9960.0340.140.877100
2.39-2.5419.10.12173160.9970.0280.1240.964100
2.54-2.7419.40.10673430.9980.0250.1090.943100
2.74-3.0118.90.09273790.9980.0220.0950.938100
3.01-3.4517.20.07874420.9980.0190.080.963100
3.45-4.3418.70.06475320.9990.0150.0661.079100
4.34-5017.30.05379310.9990.0130.0540.95399.5

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→24.93 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 14.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1731 1923 1.37 %
Rwork0.1387 138513 -
obs0.1391 140436 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.35 Å2 / Biso mean: 22.6877 Å2 / Biso min: 9.99 Å2
Refinement stepCycle: final / Resolution: 1.6→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6050 0 24 1142 7216
Biso mean--21.12 35.55 -
Num. residues----798
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2432X-RAY DIFFRACTION3.804TORSIONAL
12B2432X-RAY DIFFRACTION3.804TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.25891210.18498818893987
1.64-1.680.23631280.15639174930291
1.68-1.730.19961330.14199312944592
1.73-1.790.18471320.13519429956193
1.79-1.850.15341350.13029662979795
1.85-1.930.19431320.1369748988096
1.93-2.020.16961390.128399091004897
2.02-2.120.19551400.1272100361017698
2.12-2.250.15281390.125101141025399
2.25-2.430.19061400.1309101751031599
2.43-2.670.15951430.1386102731041699
2.67-3.060.17861450.14721036210507100
3.06-3.850.1711460.13721052210668100
3.85-24.930.15071500.14441097911129100

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