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- PDB-1fbx: CRYSTAL STRUCTURE OF ZINC-CONTAINING E.COLI GTP CYCLOHYDROLASE I -

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Basic information

Entry
Database: PDB / ID: 1fbx
TitleCRYSTAL STRUCTURE OF ZINC-CONTAINING E.COLI GTP CYCLOHYDROLASE I
ComponentsGTP CYCLOHYDROLASE I
KeywordsHYDROLASE / ALLOSTERIC ENZYME
Function / homology
Function and homology information


GTP cyclohydrolase I / GTP cyclohydrolase I activity / tetrahydrobiopterin biosynthetic process / tRNA queuosine(34) biosynthetic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / GTP binding / protein-containing complex / zinc ion binding / identical protein binding ...GTP cyclohydrolase I / GTP cyclohydrolase I activity / tetrahydrobiopterin biosynthetic process / tRNA queuosine(34) biosynthetic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / GTP binding / protein-containing complex / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I signature 2. / GTP cyclohydrolase I / GTP cyclohydrolase I, conserved site / GTP cyclohydrolase I domain / GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I / GTP cyclohydrolase I signature 1. / GTP Cyclohydrolase I; Chain A, domain 1 / GTP Cyclohydrolase I, domain 2 ...GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I signature 2. / GTP cyclohydrolase I / GTP cyclohydrolase I, conserved site / GTP cyclohydrolase I domain / GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I / GTP cyclohydrolase I signature 1. / GTP Cyclohydrolase I; Chain A, domain 1 / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GTP cyclohydrolase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsAuerbach, G. / Herrmann, A. / Bracher, A. / Bader, A. / Gutlich, M. / Fischer, M. / Neukamm, M. / Nar, H. / Garrido-Franco, M. / Richardson, J. ...Auerbach, G. / Herrmann, A. / Bracher, A. / Bader, A. / Gutlich, M. / Fischer, M. / Neukamm, M. / Nar, H. / Garrido-Franco, M. / Richardson, J. / Huber, R. / Bacher, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Zinc plays a key role in human and bacterial GTP cyclohydrolase I.
Authors: Auerbach, G. / Herrmann, A. / Bracher, A. / Bader, G. / Gutlich, M. / Fischer, M. / Neukamm, M. / Garrido-Franco, M. / Richardson, J. / Nar, H. / Huber, R. / Bacher, A.
History
DepositionJul 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / pdbx_struct_conn_angle / struct_biol / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP CYCLOHYDROLASE I
B: GTP CYCLOHYDROLASE I
C: GTP CYCLOHYDROLASE I
D: GTP CYCLOHYDROLASE I
E: GTP CYCLOHYDROLASE I
F: GTP CYCLOHYDROLASE I
G: GTP CYCLOHYDROLASE I
H: GTP CYCLOHYDROLASE I
I: GTP CYCLOHYDROLASE I
J: GTP CYCLOHYDROLASE I
K: GTP CYCLOHYDROLASE I
L: GTP CYCLOHYDROLASE I
M: GTP CYCLOHYDROLASE I
N: GTP CYCLOHYDROLASE I
O: GTP CYCLOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,51545
Polymers371,00215
Non-polymers1,51330
Water27015
1
A: GTP CYCLOHYDROLASE I
B: GTP CYCLOHYDROLASE I
C: GTP CYCLOHYDROLASE I
D: GTP CYCLOHYDROLASE I
E: GTP CYCLOHYDROLASE I
hetero molecules

A: GTP CYCLOHYDROLASE I
B: GTP CYCLOHYDROLASE I
C: GTP CYCLOHYDROLASE I
D: GTP CYCLOHYDROLASE I
E: GTP CYCLOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,34330
Polymers247,33510
Non-polymers1,00920
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_576x,-y+2,-z+11
2
F: GTP CYCLOHYDROLASE I
G: GTP CYCLOHYDROLASE I
H: GTP CYCLOHYDROLASE I
I: GTP CYCLOHYDROLASE I
J: GTP CYCLOHYDROLASE I
K: GTP CYCLOHYDROLASE I
L: GTP CYCLOHYDROLASE I
M: GTP CYCLOHYDROLASE I
N: GTP CYCLOHYDROLASE I
O: GTP CYCLOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,34330
Polymers247,33510
Non-polymers1,00920
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54560 Å2
ΔGint-607 kcal/mol
Surface area77790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.690, 314.190, 132.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a decamer

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Components

#1: Protein
GTP CYCLOHYDROLASE I / GTP-CH-I


Mass: 24733.451 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: ESCHERICHIA COLI / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6T5, GTP cyclohydrolase I
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.19 Å3/Da / Density % sol: 61.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 6000, KCL, MOPS, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
210 mMpotassium phosphate1drop
30.02 %1dropNaN3
46 %PEG60001reservoir
5150 mM1reservoirKCl
6100 mM4-morpholineprpanesulfonic1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 107321 / Num. obs: 572885 / % possible obs: 90.2 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 69.9 Å2 / Rmerge(I) obs: 0.12
Reflection shellHighest resolution: 2.8 Å / % possible all: 44.3
Reflection
*PLUS
Num. obs: 107321 / Num. measured all: 572885
Reflection shell
*PLUS
% possible obs: 44.3 %

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.8→14.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 5784233.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 5323 5 %RANDOM
Rwork0.202 ---
obs0.202 105669 91.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.64 Å2 / ksol: 0.232 e/Å3
Displacement parametersBiso mean: 52.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.1 Å20 Å20 Å2
2---7.53 Å20 Å2
3---3.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.8→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25995 0 30 15 26040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 501 5 %
Rwork0.305 9449 -
obs--52 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 52.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
LS refinement shell
*PLUS
Rfactor Rfree: 0.355 / % reflection Rfree: 5 % / Rfactor Rwork: 0.305

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