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- PDB-4rv4: 2.65 Angstrom Resolution Crystal Structure of an orotate phosphor... -

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Basic information

Entry
Database: PDB / ID: 4rv4
Title2.65 Angstrom Resolution Crystal Structure of an orotate phosphoribosyltransferase from Bacillus anthracis str. 'Ames Ancestor' in complex with 5-phospho-alpha-D-ribosyl diphosphate (PRPP)
ComponentsOrotate phosphoribosyltransferase
KeywordsTRANSFERASE / PYRIMIDINE RIBONUCLEOTIDE BIOSYNTHESIS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / GLYCOSYLTRANSFERASE / PYRIMIDINE BIOSYNTHESIS / NIAID / National Institute of Allergy and Infectious Diseases
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
DI(HYDROXYETHYL)ETHER / Chem-PRP / Orotate phosphoribosyltransferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsHalavaty, A.S. / Minasov, G. / Shuvalova, L. / Winsor, J. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.65 Angstrom resolution crystal structure of an orotate phosphoribosyltransferase from Bacillus anthracis str. 'Ames Ancestor' in complex with 5-phospho-alpha-D-ribosyl diphosphate (PRPP)
Authors: Halavaty, A.S. / Minasov, G. / Shuvalova, L. / Winsor, J. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 24, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionDec 17, 2014ID: 3OSC
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Orotate phosphoribosyltransferase
B: Orotate phosphoribosyltransferase
C: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7317
Polymers76,4553
Non-polymers1,2764
Water63135
1
A: Orotate phosphoribosyltransferase
B: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8565
Polymers50,9702
Non-polymers8863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-21 kcal/mol
Surface area17720 Å2
MethodPISA
2
C: Orotate phosphoribosyltransferase
hetero molecules

C: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7504
Polymers50,9702
Non-polymers7802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3280 Å2
ΔGint-18 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.268, 133.268, 151.348
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTHRTHRAA-2 - 20922 - 233
21SERSERTHRTHRBB-2 - 20922 - 233
12SERSERALAALAAA-2 - 21022 - 234
22SERSERALAALACC-2 - 21022 - 234
13GLNGLNALAALABB-3 - 21021 - 234
23GLNGLNALAALACC-3 - 21021 - 234

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Orotate phosphoribosyltransferase / / OPRT / OPRTase


Mass: 25484.902 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS3733, BA_4021, GBAA_4021, pyrE / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pMAGIC
References: UniProt: Q81WF6, orotate phosphoribosyltransferase
#2: Sugar ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose / Phosphoribosyl pyrophosphate


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H13O14P3
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 7 MG/ML PROTEIN IN 10 MM TRIS/HCL PH 8.0, 500 MM NACL, 5 MM BME, 10 MM 5-PHOSPHO-ALPHA-D-RIBOSYL DIPHOSPHATE (PRPP). CRYSTALS GREW FROM 0.1 M MIB BUFFER PH 4.0, 25% (W/V) PEG1500 (THE PACT ...Details: 7 MG/ML PROTEIN IN 10 MM TRIS/HCL PH 8.0, 500 MM NACL, 5 MM BME, 10 MM 5-PHOSPHO-ALPHA-D-RIBOSYL DIPHOSPHATE (PRPP). CRYSTALS GREW FROM 0.1 M MIB BUFFER PH 4.0, 25% (W/V) PEG1500 (THE PACT SUITE CONDITION #13), 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: Aug 19, 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: 2.65→30 Å / Num. all: 18197 / Num. obs: 18197 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 64.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.82
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.3 / Num. unique all: 983 / % possible all: 97.7

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3M3H

3m3h


Resolution: 2.65→29.54 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 25.386 / SU ML: 0.255 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24181 919 5.1 %RANDOM
Rwork0.19581 ---
obs0.19814 17278 89.85 %-
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: 75.808 Å2
Baniso -1Baniso -2Baniso -3
1--5.39 Å2-0 Å2-0 Å2
2---5.39 Å2-0 Å2
3---10.78 Å2
Refinement stepCycle: LAST / Resolution: 2.65→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4693 0 73 35 4801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194881
X-RAY DIFFRACTIONr_bond_other_d0.0050.024653
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.9816632
X-RAY DIFFRACTIONr_angle_other_deg1.128310766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.9235618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.54225.469192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.29615842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3481517
X-RAY DIFFRACTIONr_chiral_restr0.0960.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025423
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02988
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A11716
12B11716
21A11714
22C11714
31B11879
32C11879
LS refinement shellResolution: 2.65→2.714 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 89 -
Rwork0.294 1333 -
obs-1333 97.33 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.0750.00160.14871.8137-0.03160.8389-0.03650.1685-0.1183-0.1498-0.09860.1093-0.0167-0.0830.13510.2815-0.01750.00220.3293-0.08130.04348.0971-7.220115.5328
27.70142.86880.34663.1507-0.46931.1314-0.09610.0875-1.0091-0.2058-0.076-0.05390.0180.00830.17210.255-0.02270.01750.3135-0.12390.311148.3489-17.601615.236
312.24193.6122-1.39089.6531-3.10268.374-0.0731-0.6437-2.07230.2524-0.0461-1.21280.36010.27440.11910.06690.0675-0.0230.14190.09250.405668.9576-19.278420.1537
42.8236-0.0608-0.91920.20980.0741.42110.10780.19920.4451-0.04510.0434-0.0212-0.0572-0.06-0.15110.20580.0336-0.01730.2234-0.01940.086730.69948.552422.654
54.20661.4672-0.25562.16670.26492.08450.107-0.63510.50650.07820.0187-0.03560.00070.2411-0.12570.190.0301-0.01760.3571-0.1530.099342.77539.579431.6115
68.98630.6668-2.13361.06590.54651.00130.1777-0.31890.82450.2146-0.06160.15290.10280.0099-0.11610.230.03040.03440.2825-0.12390.11619.551412.872333.9331
74.8259-0.9113-2.84552.34330.38433.9865-0.0978-0.7541-0.07580.1008-0.05560.1682-0.37030.95090.15330.2974-0.0314-0.13770.52050.17350.209446.092846.866212.9958
82.7376-1.35-3.17725.61611.30045.7641-0.6794-0.6346-0.81180.1249-0.20750.36740.59391.00270.88680.47330.22330.08850.57520.31850.374449.868133.001111.4922
95.6136-1.4151-2.50483.70382.37154.7211-0.4009-1.9116-0.32580.78830.00170.44450.04621.01910.39920.73710.1138-0.10160.98190.18040.326939.330945.312330.2634
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 124
2X-RAY DIFFRACTION2A125 - 183
3X-RAY DIFFRACTION3A184 - 210
4X-RAY DIFFRACTION4B-7 - 95
5X-RAY DIFFRACTION5B103 - 152
6X-RAY DIFFRACTION6B153 - 210
7X-RAY DIFFRACTION7C-3 - 93
8X-RAY DIFFRACTION8C106 - 167
9X-RAY DIFFRACTION9C168 - 210

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