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- PDB-4f2g: The Crystal Structure of Ornithine carbamoyltransferase from Burk... -

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Basic information

Entry
Database: PDB / ID: 4f2g
TitleThe Crystal Structure of Ornithine carbamoyltransferase from Burkholderia thailandensis E264
ComponentsOrnithine carbamoyltransferase 1
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / carbamoyltransferase
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / citrulline biosynthetic process / L-arginine biosynthetic process via ornithine / L-arginine biosynthetic process / amino acid binding / cytoplasm
Similarity search - Function
Ornithine carbamoyltransferase / Ornithine/putrescine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain ...Ornithine carbamoyltransferase / Ornithine/putrescine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsCraig, T.K. / Fox, D. / Staker, B. / Stewart, L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMay 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Ornithine carbamoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1839
Polymers35,4561
Non-polymers7278
Water3,675204
1
A: Ornithine carbamoyltransferase 1
hetero molecules

A: Ornithine carbamoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,36618
Polymers70,9122
Non-polymers1,45416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_444-y-1/4,-x-1/4,-z-1/41
Buried area3040 Å2
ΔGint-61 kcal/mol
Surface area25110 Å2
MethodPISA
2
A: Ornithine carbamoyltransferase 1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)217,09854
Polymers212,7376
Non-polymers4,36148
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_444-y-1/4,-x-1/4,-z-1/41
crystal symmetry operation19_444-x-1/4,-z-1/4,-y-1/41
crystal symmetry operation24_444-z-1/4,-y-1/4,-x-1/41
Buried area22270 Å2
ΔGint-308 kcal/mol
Surface area62180 Å2
MethodPISA
3
A: Ornithine carbamoyltransferase 1
hetero molecules

A: Ornithine carbamoyltransferase 1
hetero molecules

A: Ornithine carbamoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,54927
Polymers106,3683
Non-polymers2,18124
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10080 Å2
ΔGint-140 kcal/mol
Surface area32140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.250, 141.250, 141.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-403-

PO4

21A-403-

PO4

31A-404-

PO4

41A-404-

PO4

51A-563-

HOH

61A-638-

HOH

71A-657-

HOH

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Components

#1: Protein Ornithine carbamoyltransferase 1 / OTCase 1


Mass: 35456.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: argF-1, argF1, BTH_I0732 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2T0L1, ornithine carbamoyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: JCSG3 well F12 0.1M Na Citrate pH5.6, 1M Ammonium dihydrogen Phosphate with 15% EG added to well solution, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→40.775 Å / Num. all: 28765 / Num. obs: 28707 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 10.96 % / Biso Wilson estimate: 27.065 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 26.41
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.150.4964.021419620861100
2.15-2.210.4025.011416120131100
2.21-2.280.3615.791447220011100
2.28-2.350.3226.57142591892199.9
2.35-2.430.2618.56153041873199.8
2.43-2.510.23610.77170131792199.9
2.51-2.60.1914.01178861734199.8
2.6-2.710.16915.99179761696199.9
2.71-2.830.15417.161770216081100
2.83-2.970.12620.811784015431100
2.97-3.130.09526.72183041494199.9
3.13-3.320.07236.4188611400199.9
3.32-3.550.06146.21208681332199.8
3.55-3.830.04956.57197581243199.9
3.83-4.20.0466.26180391144199.8
4.2-4.70.03475.72165971059199.8
4.7-5.420.03768.21144979371100
5.42-6.640.04755.38124238141100
6.64-9.390.03570.399507654199.7
9.39-40.7750.02290.435027392194.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å40.78 Å
Translation2.5 Å40.78 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PVV

1pvv


Resolution: 2.1→40.775 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8878 / SU ML: 0.17 / σ(F): 0 / Phase error: 17.42 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 1392 5.07 %random
Rwork0.1682 ---
obs0.1697 27457 95.69 %-
all-28849 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.883 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 86.33 Å2 / Biso min: 6.55 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 39 204 2534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062403
X-RAY DIFFRACTIONf_angle_d0.953273
X-RAY DIFFRACTIONf_chiral_restr0.066355
X-RAY DIFFRACTIONf_plane_restr0.003423
X-RAY DIFFRACTIONf_dihedral_angle_d13852
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1003-2.17530.21131310.21362413254490
2.1753-2.26240.19641340.19562447258192
2.2624-2.36540.24161320.1932469260192
2.3654-2.49010.20391380.18792534267294
2.4901-2.64610.24291350.18152559269496
2.6461-2.85030.20751370.18152625276297
2.8503-3.13710.18911400.17582630277097
3.1371-3.59080.19441420.15482702284499
3.5908-4.5230.17151470.13212753290099
4.523-40.7830.18461560.16412933308999
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)
16.4148-0.77310.45535.3711-2.64851.30960.26320.68630.1856-0.1709-0.12780.1249-0.1502-0.1179-0.08160.14210.0490.0080.16160.03820.1127-16.432215.8495-18.2687
24.02752.5154-2.5586.1461-0.23632.0330.01950.1699-0.1649-0.3371-0.24830.39790.0715-0.06540.14970.0820.0208-0.03720.2219-0.02240.1844-28.06295.4844-14.2808
35.50712.85921.81683.87391.36332.65060.01860.1204-0.1303-0.08860.06880.24490.07130.0269-0.05410.10970.0426-0.01270.03750.04220.1154-14.0569-1.4615-11.972
42.77381.5244-0.68183.7215-1.26021.56250.1065-0.0496-0.06160.0096-0.1099-0.1923-0.18650.1458-0.01530.08950.0110.0110.11270.00170.0622-5.08234.5124-8.0754
52.0544-0.797-0.85961.48120.56761.76410.09770.24780.1965-0.1259-0.0485-0.0537-0.13810.0281-0.0580.09930.01250.00580.09950.03390.0913-11.218112.2902-12.5174
63.1194-0.7384-0.04242.90330.31194.22690.2030.04770.3205-0.1621-0.04290.0105-0.50060.017-0.10470.16350.04950.07540.10620.03660.2199-22.824625.6814-4.5823
71.7875-0.24291.14332.0753-1.37461.58190.24640.18720.5785-0.1274-0.15380.0574-0.5671-0.0419-0.00980.30250.12630.10460.16740.04420.3247-26.413529.7792-2.3154
87.4146-5.9415-2.43686.96281.71592.0049-0.084-0.66831.0321.1330.5895-0.9137-0.91070.4776-0.48770.5001-0.00350.03230.2627-0.10540.4247-15.991626.34510.2978
92.0665-1.3118-1.03093.1381.22563.02470.0372-0.18590.16850.27540.02450.1468-0.0929-0.0269-0.04350.15340.04380.06920.1644-0.01390.1676-26.424819.26429.5109
101.2611-0.7331-1.27832.21031.47893.4732-0.00020.1585-0.0492-0.0657-0.04530.1885-0.0043-0.30470.02270.06790.0044-0.0190.12590.01020.143-21.67885.6996-9.4203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:16)A6 - 16
2X-RAY DIFFRACTION2chain 'A' and (resseq 17:35)A17 - 35
3X-RAY DIFFRACTION3chain 'A' and (resseq 36:56)A36 - 56
4X-RAY DIFFRACTION4chain 'A' and (resseq 57:91)A57 - 91
5X-RAY DIFFRACTION5chain 'A' and (resseq 92:149)A92 - 149
6X-RAY DIFFRACTION6chain 'A' and (resseq 150:194)A150 - 194
7X-RAY DIFFRACTION7chain 'A' and (resseq 195:222)A195 - 222
8X-RAY DIFFRACTION8chain 'A' and (resseq 223:244)A223 - 244
9X-RAY DIFFRACTION9chain 'A' and (resseq 245:283)A245 - 283
10X-RAY DIFFRACTION10chain 'A' and (resseq 284:307)A284 - 307

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