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- PDB-2bz1: CRYSTAL STRUCTURE OF APO E. COLI GTP CYCLOHYDROLASE II -

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Basic information

Entry
Database: PDB / ID: 2bz1
TitleCRYSTAL STRUCTURE OF APO E. COLI GTP CYCLOHYDROLASE II
ComponentsGTP CYCLOHYDROLASE II
KeywordsHYDROLASE / RIBOFLAVIN BIOSYNTHESIS / GTP CYCLOHYDROLASE II / CATALYTIC ZINC / MAGNESIUM
Function / homology
Function and homology information


GTP cyclohydrolase II / GTP cyclohydrolase II activity / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / GTP binding / magnesium ion binding / protein homodimerization activity / zinc ion binding / cytosol
Similarity search - Function
GTP cyclohydrolase II / GTP cyclohydrolase II, RibA / GTP cyclohydrolase II / GTP cyclohydrolase II superfamily / GTP cyclohydrolase II / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-AMINOETHANESULFONIC ACID / GTP cyclohydrolase-2
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.54 Å
AuthorsRen, J. / Kotaka, M. / Lockyer, M. / Lamb, H.K. / Hawkins, A.R. / Stammers, D.K.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: GTP Cyclohydrolase II Structure and Mechanism.
Authors: Ren, J. / Kotaka, M. / Lockyer, M. / Lamb, H.K. / Hawkins, A.R. / Stammers, D.K.
History
DepositionAug 9, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP CYCLOHYDROLASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6227
Polymers22,0521
Non-polymers5716
Water3,657203
1
A: GTP CYCLOHYDROLASE II
hetero molecules

A: GTP CYCLOHYDROLASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,24514
Polymers44,1032
Non-polymers1,14212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
MethodPQS
Unit cell
Length a, b, c (Å)71.920, 71.920, 128.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2087-

HOH

21A-2202-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GTP CYCLOHYDROLASE II


Mass: 22051.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PRETB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A7I7, GTP cyclohydrolase II

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Non-polymers , 5 types, 209 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TAU / 2-AMINOETHANESULFONIC ACID


Mass: 125.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7NO3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.2 Å3/Da / Density % sol: 43.59 %
Crystal growpH: 7
Details: 1.5M AMMONIUM SULPHATE, 0.1M NA HEPES PH 7.0, 2% PEG 400, 15% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97912
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.54→30 Å / Num. obs: 27407 / % possible obs: 89.4 % / Observed criterion σ(I): 0 / Redundancy: 17.2 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 76.4
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.3 / % possible all: 26.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.54→28.57 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2026961.74 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: RESIDUAL, MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1334 4.9 %RANDOM
Rwork0.193 ---
obs0.193 27331 91.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.69 Å2 / ksol: 0.367015 e/Å3
Displacement parametersBiso mean: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.06 Å20 Å2
2--0.34 Å20 Å2
3----0.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.54→28.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1348 0 29 203 1580
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.344
X-RAY DIFFRACTIONc_mcangle_it36
X-RAY DIFFRACTIONc_scbond_it4.696
X-RAY DIFFRACTIONc_scangle_it6.0112
LS refinement shellResolution: 1.54→1.64 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 139 5.7 %
Rwork0.261 2320 -
obs--50.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP

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