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- PDB-2r5r: The crystal structure of DUF198 from Nitrosomonas europaea ATCC 19718 -

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Basic information

Entry
Database: PDB / ID: 2r5r
TitleThe crystal structure of DUF198 from Nitrosomonas europaea ATCC 19718
ComponentsUPF0343 protein NE1163
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC86493 / DUF198 / Nitrosomonas europaea ATCC 19718 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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
IMIDAZOLE / PHOSPHATE ION / GTP cyclohydrolase FolE2
Similarity search - Component
Biological speciesNitrosomonas europaea ATCC 19718 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.05 Å
AuthorsTan, K. / Wu, R. / Nocek, B. / Bigelow, L. / Patterson, S. / Freeman, L. / Bargassa, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of DUF198 from Nitrosomonas europaea ATCC 19718.
Authors: Tan, K. / Wu, R. / Nocek, B. / Bigelow, L. / Patterson, S. / Freeman, L. / Bargassa, M. / Joachimiak, A.
History
DepositionSep 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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 NE1163
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3653
Polymers31,2011
Non-polymers1642
Water00
1
A: UPF0343 protein NE1163
hetero molecules

A: UPF0343 protein NE1163
hetero molecules

A: UPF0343 protein NE1163
hetero molecules

A: UPF0343 protein NE1163
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,46212
Polymers124,8054
Non-polymers6568
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.705, 118.705, 113.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsAuthors state that the biological unit is experimentally unknown. From molecular packing, it seems to be a tetramer, generated from symmetry operators given in remark 350.

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Components

#1: Protein UPF0343 protein NE1163


Mass: 31201.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea ATCC 19718 (bacteria)
Species: Nitrosomonas europaea / Strain: IFO 14298 / Gene: NE1163 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q82VD1
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
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: 3.69 Å3/Da / Density % sol: 66.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 1.6M NaH2PO4/0.4M K2HPO4, 0.1M Phosphate-Citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97951, 0.97965
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2007 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979511
20.979651
ReflectionResolution: 3.05→38.87 Å / Num. all: 9363 / Num. obs: 9363 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 17.4
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 1.6 / Num. unique all: 846 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
DMphasing
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 3.05→38.87 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.902 / SU B: 17.744 / SU ML: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.083 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26052 445 4.8 %RANDOM
Rwork0.23905 ---
all0.24007 8890 --
obs0.24007 8890 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.918 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 3.05→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1978 0 10 0 1988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222030
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0071.9382744
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3425245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96323.824102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02215353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.251514
X-RAY DIFFRACTIONr_chiral_restr0.0760.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021544
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.2891
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21402
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0370.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4191.51258
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.75121997
X-RAY DIFFRACTIONr_scbond_it0.5593854
X-RAY DIFFRACTIONr_scangle_it1.0114.5747
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.05→3.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 35 -
Rwork0.352 578 -
obs-613 91.49 %

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