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- PDB-5k9g: Crystal Structure of GTP Cyclohydrolase-IB with Tris -

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Basic information

Entry
Database: PDB / ID: 5k9g
TitleCrystal Structure of GTP Cyclohydrolase-IB with Tris
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
FORMIC ACID / GTP cyclohydrolase FolE2
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAlvarez, J. / Stec, B. / Swairjo, M.A.
Citation
Journal: 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.
#1: Journal: J.Bacteriol. / Year: 2009
Title: Zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for GTP cyclohydrolase IB.
Authors: Sankaran, B. / Bonnett, S.A. / Shah, K. / Gabriel, S. / Reddy, R. / Schimmel, P. / Rodionov, D.A. / de Crecy-Lagard, V. / Helmann, J.D. / Iwata-Reuyl, D. / Swairjo, M.A.
History
DepositionMay 31, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionSep 7, 2016ID: 3D1T
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_database_PDB_obs_spr / pdbx_struct_oper_list / pdbx_struct_special_symmetry
Item: _pdbx_database_PDB_obs_spr.replace_pdb_id / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 27, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.3Feb 1, 2023Group: Advisory / Category: pdbx_database_PDB_obs_spr / Item: _pdbx_database_PDB_obs_spr.replace_pdb_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,41914
Polymers57,6242
Non-polymers79612
Water6,900383
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)116,83828
Polymers115,2474
Non-polymers1,59124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area20680 Å2
ΔGint-37 kcal/mol
Surface area35170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.707, 100.557, 114.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-54-

GLU

21B-501-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 395 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C4H12NO3 / References: GTP cyclohydrolase I / Comment: pH buffer*YM
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: (PEG 6000, 10-16%), LiCl (1-1.4 M), Tris (50 mM, pH 9.0) and Tris-Cl (50 mM, pH 7.0). Enzym sample prepared at 10 mg/mL in 50 mM Tris-HCl, 50 mM KCl, 1 mM DTT, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9767 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9767 Å / Relative weight: 1
ReflectionResolution: 1.9→68.16 Å / Num. obs: 41832 / % possible obs: 99.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 36.17
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.05

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D1T

3d1t
PDB Unreleased entry


Resolution: 1.9→68.16 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.63 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22079 2068 4.9 %RANDOM
Rwork0.17305 ---
obs0.17537 39731 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.031 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å2-0 Å20 Å2
2--0.62 Å2-0 Å2
3---1.7 Å2
Refinement stepCycle: LAST / Resolution: 1.9→68.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3841 0 45 383 4269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194112
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.9715581
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9635.019533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55923.889180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48415733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7021525
X-RAY DIFFRACTIONr_chiral_restr0.1730.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213070
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.6983.8692009
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.4165.7762523
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7864.2772103
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.01933.9166517
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: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 158 -
Rwork0.265 2643 -
obs--91.57 %

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