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- PDB-3d2o: Crystal Structure of Manganese-metallated GTP Cyclohydrolase Type IB -

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Basic information

Entry
Database: PDB / ID: 3d2o
TitleCrystal Structure of Manganese-metallated GTP Cyclohydrolase Type IB
ComponentsUPF0343 protein NGO0387
KeywordsHYDROLASE / BIOSYNTHETIC PROTEIN / bimodular Tunnel Fold / Tunneling Fold / Folate Biosynthesis / GTP Cyclohydrolase / metalloenzyme / manganese
Function / homology
Function and homology information


GTP cyclohydrolase I / GTP cyclohydrolase I activity
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
AZIDE ION / : / : / GTP cyclohydrolase FolE2
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.04 Å
AuthorsSwairjo, M.A.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 2006
Title: Discovery of a New Prokaryotic Type I GTP Cyclohydrolase Family
Authors: El Yacoubi, B. / Bonnett, S. / Anderson, J.A. / Swairjo, M.A. / Iwata-Reuyl, D. / de Crecy-Lagard, V.
History
DepositionMay 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_label_asym_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: UPF0343 protein NGO0387
B: UPF0343 protein NGO0387
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7607
Polymers57,5662
Non-polymers1945
Water4,702261
1
A: UPF0343 protein NGO0387
B: UPF0343 protein NGO0387
hetero molecules

A: UPF0343 protein NGO0387
B: UPF0343 protein NGO0387
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,52014
Polymers115,1314
Non-polymers38910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area18350 Å2
ΔGint-126.4 kcal/mol
Surface area35190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.225, 100.420, 113.947
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-315-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein UPF0343 protein NGO0387


Mass: 28782.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: expression vector pET-30 Xa/LIC with Factor Xa-cleavable His6 tag
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: ngo0387 / Plasmid: pSAB-8-142 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5F9K6, GTP cyclohydrolase I

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Non-polymers , 5 types, 266 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
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, VAPOR DIFFUSION, ...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, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97607 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2008
RadiationMonochromator: single crystal (Si111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97607 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. all: 33675 / Num. obs: 33675 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.071 / Χ2: 1.06 / Net I/σ(I): 11
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.428 / Num. unique all: 3314 / Χ2: 0.81 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3D1T

3d1t
PDB Unreleased entry


Resolution: 2.04→30.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.475 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1710 5.1 %RANDOM
Rwork0.185 ---
obs0.189 33647 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.382 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.04→30.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3829 0 7 261 4097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223905
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.9665285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9625485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18523.964169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60415695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3311523
X-RAY DIFFRACTIONr_chiral_restr0.1220.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022901
X-RAY DIFFRACTIONr_nbd_refined0.220.21702
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22678
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2252
X-RAY DIFFRACTIONr_metal_ion_refined0.1810.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.2126
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.221
X-RAY DIFFRACTIONr_mcbond_it1.421.52522
X-RAY DIFFRACTIONr_mcangle_it2.18423954
X-RAY DIFFRACTIONr_scbond_it3.2931570
X-RAY DIFFRACTIONr_scangle_it4.4514.51331
X-RAY DIFFRACTIONr_rigid_bond_restr2.30234092
X-RAY DIFFRACTIONr_sphericity_free8.8423272
X-RAY DIFFRACTIONr_sphericity_bonded4.39133832
LS refinement shellResolution: 2.04→2.097 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 127 -
Rwork0.191 2251 -
all-2378 -
obs--98.02 %

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