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- PDB-3m3h: 1.75 Angstrom resolution crystal structure of an orotate phosphor... -

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Basic information

Entry
Database: PDB / ID: 3m3h
Title1.75 Angstrom resolution crystal structure of an orotate phosphoribosyltransferase from Bacillus anthracis str. 'Ames Ancestor'
ComponentsOrotate phosphoribosyltransferase
KeywordsTRANSFERASE / Orotate Phosphoribosyltransferase / Pyrimidine Ribonucleotide Biosynthesis / Structural Genomics / Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Glycosyltransferase / Magnesium / Pyrimidine biosynthesis
Function / homology
Function and homology information


orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / 'de novo' UMP biosynthetic process / magnesium ion binding
Similarity search - Function
Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Orotate phosphoribosyltransferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHalavaty, A.S. / Shuvalova, L. / Minasov, G. / Winsor, J. / Dubrovska, I. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.75 Angstrom resolution crystal structure of an orotate phosphoribosyltransferase from Bacillus anthracis str. 'Ames Ancestor'
Authors: Halavaty, A.S. / Shuvalova, L. / Minasov, G. / Winsor, J. / Dubrovska, I. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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_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_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

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Assembly

Deposited unit
A: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7338
Polymers25,4851
Non-polymers2487
Water1,982110
1
A: Orotate phosphoribosyltransferase
hetero molecules

A: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,46616
Polymers50,9702
Non-polymers49614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3820 Å2
ΔGint-145 kcal/mol
Surface area17350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.762, 56.762, 113.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Orotate phosphoribosyltransferase / / OPRT / OPRTase


Mass: 25484.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: 'Ames Ancestor' / Gene: pyrE, BA_4021, GBAA_4021, BAS3733 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus
References: UniProt: Q81WF6, orotate phosphoribosyltransferase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 1.8 Å3/Da / Density % sol: 31.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 7.7 mg/mL in 10 mM Tris/HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Classic II condition (CS2) A8 (#8). Cryo condition 2.5 M KCl and 25% sucrose. VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 4, 2010 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 19414 / Num. obs: 19414 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 27.8
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 5.7 / Num. unique all: 960 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DEZ
Resolution: 1.75→28.43 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.713 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22285 990 5.1 %RANDOM
Rwork0.1792 ---
obs0.18136 18360 99.42 %-
all-18360 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.589 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2---0.76 Å2-0 Å2
3---1.52 Å2
Refinement stepCycle: LAST / Resolution: 1.75→28.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 7 110 1663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221680
X-RAY DIFFRACTIONr_bond_other_d00.021117
X-RAY DIFFRACTIONr_angle_refined_deg1.281.962291
X-RAY DIFFRACTIONr_angle_other_deg0.77832759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3415223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.98625.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.59615298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.885157
X-RAY DIFFRACTIONr_chiral_restr0.0810.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021927
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02316
X-RAY DIFFRACTIONr_mcbond_it0.8431.51073
X-RAY DIFFRACTIONr_mcbond_other0.2311.5434
X-RAY DIFFRACTIONr_mcangle_it1.64321737
X-RAY DIFFRACTIONr_scbond_it2.7663607
X-RAY DIFFRACTIONr_scangle_it4.5954.5554
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 79 -
Rwork0.182 1321 -
obs-1321 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.3104-0.5975-0.11642.9836-0.20751.2459-0.0241-0.1293-0.0309-0.03430.0261-0.02530.03780.0399-0.0020.0768-0.0191-0.00130.08690.00860.00637.469820.856836.2703
21.13920.25470.40661.2230.43193.22950.0437-0.0244-0.1558-0.057-0.0015-0.18170.05220.1072-0.04210.02640.00510.00150.01470.00110.046723.923822.33924.732
31.8850.14640.53541.7536-0.72981.0493-0.07250.10080.2523-0.13190.06090.1103-0.1334-0.040.01160.12160.0008-0.00910.0428-0.00050.051115.551530.581716.3787
40.97780.3045-1.19250.7241-0.7452.1961-0.04540.0191-0.0875-0.03210.06890.1470.1295-0.2911-0.02350.0854-0.0352-0.00780.11670.02250.06120.7517.058929.7464
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 38
2X-RAY DIFFRACTION2A39 - 90
3X-RAY DIFFRACTION3A91 - 150
4X-RAY DIFFRACTION4A151 - 210

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