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- PDB-5k95: Crystal Structure of GTP Cyclohydrolase-IB with 8-oxo-GTP -

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Basic information

Entry
Database: PDB / ID: 5k95
TitleCrystal Structure of GTP Cyclohydrolase-IB with 8-oxo-GTP
ComponentsGTP cyclohydrolase FolE2
KeywordsHYDROLASE / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


GTP cyclohydrolase I / GTP cyclohydrolase I activity / tetrahydrofolate biosynthetic process
Similarity search - Function
GTP cyclohydrolase FolE2/MptA / GTP cyclohydrolase FolE2 / Type I GTP cyclohydrolase folE2 / Urate Oxidase / Urate Oxidase; / Roll / Alpha Beta
Similarity search - Domain/homology
8-OXO-GUANOSINE-5'-TRIPHOSPHATE / GTP cyclohydrolase FolE2
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsAlvarez, J. / Stec, B. / Swairjo, M.A.
CitationJournal: Biochem.J. / Year: 2017
Title: Mechanism and catalytic strategy of the prokaryotic-specific GTP cyclohydrolase-IB.
Authors: Paranagama, N. / Bonnett, S.A. / Alvarez, J. / Luthra, A. / Stec, B. / Gustafson, A. / Iwata-Reuyl, D. / Swairjo, M.A.
History
DepositionMay 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_symmetry
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP cyclohydrolase FolE2
B: GTP cyclohydrolase FolE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2284
Polymers57,6242
Non-polymers6052
Water2,000111
1
A: GTP cyclohydrolase FolE2
B: GTP cyclohydrolase FolE2
hetero molecules

A: GTP cyclohydrolase FolE2
B: GTP cyclohydrolase FolE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4578
Polymers115,2474
Non-polymers1,2094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area18360 Å2
ΔGint-145 kcal/mol
Surface area38080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.876, 100.557, 115.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein GTP cyclohydrolase FolE2 / GTP cyclohydrolase 1B


Mass: 28811.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (bacteria)
Strain: ATCC 700825 / FA 1090 / Gene: folE2, NGO0387 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5F9K6, GTP cyclohydrolase I
#2: Chemical ChemComp-8GT / 8-OXO-GUANOSINE-5'-TRIPHOSPHATE


Mass: 539.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O15P3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 10-16% polyethylene glycol 6000, 0.6-1.4 M LiCl, 60 mM HEPES pH 8.2, 40 mM HEPES

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.77→46.07 Å / Num. obs: 13898 / % possible obs: 99.7 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 10.4
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.833

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D1T

3d1t
PDB Unreleased entry


Resolution: 2.77→46.07 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.88 / SU B: 13.34 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2768 684 5 %RANDOM
Rwork0.17492 ---
obs0.18012 12954 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.584 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.77→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3860 0 34 111 4005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024049
X-RAY DIFFRACTIONr_bond_other_d0.0010.022725
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9795501
X-RAY DIFFRACTIONr_angle_other_deg0.85336668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6125505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05223.807176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.71915718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1871526
X-RAY DIFFRACTIONr_chiral_restr0.0730.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02803
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.77→2.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 32 -
Rwork0.303 722 -
obs--78.79 %

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