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- PDB-4ohc: Crystal structure of orotate phosphoribosyltransferase (OPRTase) ... -

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Basic information

Entry
Database: PDB / ID: 4ohc
TitleCrystal structure of orotate phosphoribosyltransferase (OPRTase) from Burkholderia cenocepacia
ComponentsOrotate phosphoribosyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / OPRT / OPRTase
Function / homology
Function and homology information


orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / nucleoside metabolic process / 'de novo' UMP biosynthetic process / magnesium ion binding
Similarity search - Function
Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Orotate phosphoribosyltransferase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of orotate phosphoribosyltransferase (OPRTase) from Burkholderia cenocepacia
Authors: Lukacs, C.M. / Abendroth, J. / Edwards, T.E. / Lorimer, D.
History
DepositionJan 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_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_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: Orotate phosphoribosyltransferase
B: Orotate phosphoribosyltransferase
C: Orotate phosphoribosyltransferase
D: Orotate phosphoribosyltransferase
E: Orotate phosphoribosyltransferase
F: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,24823
Polymers159,3686
Non-polymers88117
Water21,1681175
1
A: Orotate phosphoribosyltransferase
D: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5099
Polymers53,1232
Non-polymers3867
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-9 kcal/mol
Surface area19570 Å2
MethodPISA
2
B: Orotate phosphoribosyltransferase
E: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4118
Polymers53,1232
Non-polymers2886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-24 kcal/mol
Surface area19550 Å2
MethodPISA
3
C: Orotate phosphoribosyltransferase
F: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3296
Polymers53,1232
Non-polymers2064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-16 kcal/mol
Surface area19400 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17130 Å2
ΔGint-51 kcal/mol
Surface area50080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.310, 82.970, 83.100
Angle α, β, γ (deg.)105.83, 104.27, 117.36
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Orotate phosphoribosyltransferase / OPRT / OPRTase


Mass: 26561.299 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: pyrE, BCAL0204 / Production host: Escherichia coli (E. coli)
References: UniProt: B4E589, orotate phosphoribosyltransferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1175 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: JCSG+ g6: 200mM sodium malonate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionHighest resolution: 1.85 Å / Num. all: 134209 / Num. obs: 130679 / % possible obs: 97.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 17.7 Å2 / Rsym value: 0.06 / Net I/σ(I): 17.9
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.75 / Num. unique all: 9459 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3m3h
Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.188 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19659 6564 5 %RANDOM
Rwork0.15556 ---
obs0.15758 124114 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.629 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.06 Å20.24 Å2
2--0.51 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10303 0 56 1175 11534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01910738
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210096
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.93414618
X-RAY DIFFRACTIONr_angle_other_deg0.852323114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03951377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28923.172476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.985151696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0291574
X-RAY DIFFRACTIONr_chiral_restr0.0990.21651
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212247
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022571
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_it1.0040.5645379
X-RAY DIFFRACTIONr_mcbond_other0.9910.5595372
X-RAY DIFFRACTIONr_mcangle_it1.6650.8266717
X-RAY DIFFRACTIONr_mcangle_other1.6650.8276718
X-RAY DIFFRACTIONr_scbond_it0.9210.615359
X-RAY DIFFRACTIONr_scbond_other0.9210.6115360
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4620.8867876
X-RAY DIFFRACTIONr_long_range_B_refined7.7876.29413196
X-RAY DIFFRACTIONr_long_range_B_other7.7866.29713197
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 494 -
Rwork0.243 8957 -
obs--95.99 %
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)
13.8414-0.30760.06074.56161.34342.2804-0.02010.2501-0.1367-0.0497-0.04130.2799-0.0431-0.1190.06140.129-0.0309-0.01270.24650.00270.1678-62.5341-28.4251-25.5956
21.1161-2.7941-2.35598.25262.68215.0751-0.5836-0.2394-0.07981.29320.91660.25481.16150.3119-0.33310.4993-0.0729-0.03910.34-0.09190.5588-73.1258-44.4787-16.8293
30.7521-0.4730.44290.64980.26341.1334-0.02290.0209-0.05550.02940.01190.10530.03840.00870.0110.1307-0.03570.00630.170.00680.1805-51.8246-29.9361-14.2252
49.08522.1128-5.95741.4769-5.454320.75540.4855-1.32490.0406-0.1089-0.18740.09470.53470.5138-0.2980.3027-0.0117-0.02580.32790.05110.3594-53.6036-42.34915.7785
52.3394-0.33331.59070.6071-0.54672.9179-0.0121-0.0861-0.08980.06830.04380.12090.0479-0.1652-0.03180.1323-0.01720.01890.16120.01290.1749-62.1719-29.313-9.783
62.9198-4.6659-0.63647.55780.80840.6838-0.10690.1477-0.90470.3177-0.00531.5104-0.389-0.35690.11220.39350.07870.0780.57530.09720.4976-79.6495-35.5834-20.391
74.440.5942-0.03681.38260.25981.7532-0.0908-0.09350.32390.02390.0255-0.1541-0.04450.1090.06520.14050.0101-0.02980.19870.01130.2238-7.379-11.8403-16.1943
80.86460.072-0.7960.5488-0.74891.62250.01020.0105-0.01110.0357-0.0223-0.0539-0.0194-0.00630.01210.1354-0.0312-0.02890.1642-0.00860.177-25.4461-16.2111-10.4006
90.2771-1.0245-0.66587.0631.21052.45960.0114-0.13920.03110.42280.17070.191-0.370.1839-0.18210.2466-0.01350.01820.3433-0.07620.1941-28.3041-8.11432.397
106.8992-3.7549-7.56436.13468.788713.63230.2404-0.55720.15540.1938-0.0466-0.11260.09180.244-0.19380.2647-0.0678-0.07670.29610.04380.3419-12.5924-9.38851.2265
113.1606-0.3239-1.98670.52720.40712.1832-0.0369-0.3163-0.00470.1469-0.0239-0.1582-0.01870.20040.06090.166-0.0181-0.05640.21330.01370.1896-12.7195-16.7404-3.2
121.9901-0.7331-2.92792.7731.64394.53080.0293-0.2110.1072-0.12840.0229-0.1686-0.12320.4207-0.05220.099-0.023-0.07160.32610.02770.36115.3862-11.4675-14.1994
132.101-2.9963-8.34074.299311.956333.2642-0.4665-0.2572-0.04410.76680.26270.05632.050.72270.20380.6354-0.1975-0.17630.6133-0.03050.1023-15.047-34.9862-26.1533
141.8746-0.9183-1.19053.92571.02150.98420.06730.3568-0.4437-0.3538-0.2216-0.09420.0947-0.16250.15430.2950.04750.00150.2494-0.10430.2778-23.2959-44.8991-42.7993
151.64181.02660.08051.9666-0.24130.29390.03150.0155-0.00980.0549-0.02580.01290.11440.0936-0.00570.1621-0.00840.01630.1765-0.01080.1276-25.5397-27.059-34.988
162.0446-0.5236-0.74791.92111.12439.91910.06010.23910.0893-0.2992-0.02320.0422-0.29170.0141-0.03680.1945-0.0086-0.01690.20260.00250.2461-26.3664-18.0234-46.9495
170.8589-0.1908-0.23493.7483-1.49211.7071-0.04290.1521-0.0798-0.1854-0.0724-0.27480.09620.18090.11530.1670.00250.02410.2472-0.00520.1864-15.8703-28.1304-43.9689
182.7401-0.66621.26531.86930.02420.68120.15990.3752-0.51250.02540.0517-0.19320.08550.2582-0.21160.35070.09860.11330.2494-0.03730.4137-14.2038-52.5793-46.2951
1916.135520.174-25.91225.2556-32.426741.6472-0.6964-2.0719-1.9268-1.0099-2.5815-2.58581.18663.36723.27790.9857-0.150.72980.73480.19481.251-21.1915-41.3864-16.0731
201.49091.3734-0.62822.6956-3.14235.0362-0.0293-0.1225-0.10.0479-0.0236-0.03440.0404-0.05450.05290.20270.04270.03650.19710.02480.1976-32.1206-45.2893.5246
210.7524-0.49910.16581.04180.82871.9384-0.0877-0.0743-0.019-0.0777-0.0042-0.01670.02010.06550.09190.1758-0.00890.01170.14980.02140.1646-37.0484-38.7832-14.8315
225.2553.5514-2.46375.5664-2.74773.5096-0.0940.1287-0.1209-0.17970.10470.33480.3329-0.4018-0.01070.2036-0.032-0.01420.2098-0.03610.2413-51.2074-46.6393-19.3405
231.39460.20850.54351.90530.5341.6428-0.05640.0289-0.22360.04190.00950.0820.3142-0.1480.04690.2376-0.03220.04710.1353-0.01080.2126-41.1601-52.0276-16.5596
240.862-0.26620.67270.9552-0.73362.5226-0.034-0.1085-0.1366-0.0006-0.0526-0.13280.22980.21890.08660.18820.05230.05930.18130.06050.2151-27.3685-52.2923-0.9054
2526.435329.558730.471133.056834.071235.1262-0.6108-2.54872.9975-0.7262-2.87063.3678-0.681-2.94563.48140.52230.0831-0.03680.5613-0.33410.627-51.3666-4.8336-24.0018
262.9856-1.5197-1.78392.96511.53532.5495-0.1916-0.25340.26810.31550.15160.0693-0.0994-0.16680.040.2140.02730.00310.1933-0.01850.2606-48.8706-1.0961-4.8272
2722.77184.511-18.07211.9113-2.719215.0761.2898-0.52120.88570.0285-0.4443-0.0435-1.2370.0695-0.84550.28390.2829-0.11160.677-0.11660.4405-40.418913.76450.3729
281.5155-0.0516-0.72250.1585-0.34991.3241-0.0079-0.08680.09570.0194-0.0344-0.0171-0.11980.03360.04230.1704-0.005-0.02270.1561-0.02640.1888-33.8658-4.0168-16.5046
291.60750.061.25741.6905-0.71391.3292-0.11770.16730.08910.1425-0.0282-0.1547-0.18240.17280.14590.1983-0.06540.00140.1815-0.03350.2383-28.12624.1403-19.6968
302.5759-0.5935-1.18040.73280.16271.38840.1028-0.06310.32740.0595-0.00860.0611-0.2697-0.0856-0.09410.20980.02110.00070.1491-0.03040.2572-44.74278.1676-13.0621
310.01660.039-0.26922.2916-12.344366.81020.1789-0.10390.00210.39210.86850.2557-1.8305-3.2614-1.04740.80670.24820.44881.06140.14570.2503-54.3563-13.4313-33.4495
320.65850.2652-0.93172.2359-1.94526.1522-0.01440.17170.1162-0.14750.0265-0.0313-0.0844-0.0369-0.01210.18670.0102-0.00730.22050.04890.1868-41.8321-5.5494-51.1294
331.80410.9750.20731.9944-0.01340.37620.04590.0870.08070.0326-0.0178-0.03020.0099-0.1326-0.02810.1599-0.0189-0.01060.1930.01650.117-41.8341-21.4047-38.4977
341.76710.1448-1.37461.88951.20577.9387-0.07570.2156-0.2611-0.23130.1-0.10680.3548-0.0759-0.02440.2389-0.0266-0.01670.2333-0.03670.2609-38.1765-34.8602-47.1139
350.8508-0.1016-0.18073.3652-0.36341.0532-0.03980.24960.0072-0.21090.08610.10930.1032-0.2182-0.04620.1707-0.0511-0.03770.30710.01320.144-49.8932-20.9751-49.2782
361.7186-0.6414-0.41483.18870.93582.375-0.07840.05810.3499-0.15040.01010.2163-0.4384-0.35120.06830.30440.0545-0.02090.31230.10270.2128-49.24731.0823-56.4453
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 25
2X-RAY DIFFRACTION2A26 - 34
3X-RAY DIFFRACTION3A35 - 101
4X-RAY DIFFRACTION4A102 - 110
5X-RAY DIFFRACTION5A111 - 199
6X-RAY DIFFRACTION6A200 - 219
7X-RAY DIFFRACTION7B2 - 44
8X-RAY DIFFRACTION8B45 - 102
9X-RAY DIFFRACTION9B103 - 129
10X-RAY DIFFRACTION10B130 - 138
11X-RAY DIFFRACTION11B139 - 192
12X-RAY DIFFRACTION12B193 - 219
13X-RAY DIFFRACTION13C2 - 5
14X-RAY DIFFRACTION14C6 - 44
15X-RAY DIFFRACTION15C45 - 91
16X-RAY DIFFRACTION16C92 - 110
17X-RAY DIFFRACTION17C111 - 192
18X-RAY DIFFRACTION18C193 - 219
19X-RAY DIFFRACTION19D2 - 4
20X-RAY DIFFRACTION20D5 - 42
21X-RAY DIFFRACTION21D43 - 91
22X-RAY DIFFRACTION22D92 - 117
23X-RAY DIFFRACTION23D118 - 158
24X-RAY DIFFRACTION24D159 - 219
25X-RAY DIFFRACTION25E2 - 4
26X-RAY DIFFRACTION26E5 - 29
27X-RAY DIFFRACTION27E30 - 35
28X-RAY DIFFRACTION28E36 - 109
29X-RAY DIFFRACTION29E110 - 136
30X-RAY DIFFRACTION30E137 - 218
31X-RAY DIFFRACTION31F2 - 5
32X-RAY DIFFRACTION32F6 - 42
33X-RAY DIFFRACTION33F43 - 90
34X-RAY DIFFRACTION34F91 - 118
35X-RAY DIFFRACTION35F119 - 193
36X-RAY DIFFRACTION36F194 - 219

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