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- PDB-3lxm: 2.00 Angstrom resolution crystal structure of a catalytic subunit... -

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Basic information

Entry
Database: PDB / ID: 3lxm
Title2.00 Angstrom resolution crystal structure of a catalytic subunit of an aspartate carbamoyltransferase (pyrB) from Yersinia pestis CO92
ComponentsAspartate carbamoyltransferase
KeywordsTRANSFERASE / Aspartate Carbamoyltransferase Catalytic Subunit / Yersinia pestis CO92 / Infectious Diseases / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Pyrimidine biosynthesis
Function / homology
Function and homology information


aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / : / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytosol / cytoplasm
Similarity search - Function
Aspartate/ornithine carbamoyltransferase / Aspartate 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 ...Aspartate/ornithine carbamoyltransferase / Aspartate 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
Aspartate carbamoyltransferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHalavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.00 Angstrom resolution crystal structure of a catalytic subunit of an aspartate carbamoyltransferase (pyrB) from Yersinia pestis CO92
Authors: Halavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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

Downloads & links

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Assembly

Deposited unit
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase
C: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,2214
Polymers112,0273
Non-polymers1941
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-18 kcal/mol
Surface area32970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.620, 120.409, 126.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aspartate carbamoyltransferase / / Aspartate transcarbamylase / ATCase


Mass: 37342.254 Da / Num. of mol.: 3 / Fragment: aspartate carbamoyltransferase catalytic subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: pyrB, y0161, YPO3588, YP_3842 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus / References: UniProt: Q8ZB39, aspartate carbamoyltransferase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 7.4 mg/mL protein in 10 mM Tris/HCl pH 8.3, 0.25 M NaCl, 5 mM BME; The JCSG+ condition #2 (0.1 M tri-sodium citrate, 20% (w/v) PEG 3000), VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2010 / Details: beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 70940 / Num. obs: 70940 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 20.28
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 3.39 / Num. unique all: 3480 / % 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: 1EKX

1ekx


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.948 / SU ML: 0.101 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21694 3574 5 %RANDOM
Rwork0.17943 ---
obs0.18134 67286 99.69 %-
all-67286 --
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: 45.809 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å2-0 Å2
2--1.59 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6731 0 13 452 7196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226876
X-RAY DIFFRACTIONr_bond_other_d0.0010.024554
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.9669336
X-RAY DIFFRACTIONr_angle_other_deg0.924311150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7915857
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22524.34318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.484151169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6271541
X-RAY DIFFRACTIONr_chiral_restr0.1130.21087
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217642
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021355
X-RAY DIFFRACTIONr_mcbond_it1.0121.54284
X-RAY DIFFRACTIONr_mcbond_other0.3211.51718
X-RAY DIFFRACTIONr_mcangle_it1.68726926
X-RAY DIFFRACTIONr_scbond_it2.58532592
X-RAY DIFFRACTIONr_scangle_it3.894.52410
LS refinement shellResolution: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 240 -
Rwork0.237 4840 -
obs-4840 98.09 %
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)
13.56670.0335-1.07541.9203-0.12023.6646-0.02460.07290.17760.0180.0406-0.1329-0.18040.0509-0.01590.059-0.0071-0.0260.0335-0.03050.118146.2926106.096616.0524
23.1887-1.4824-1.78012.0731.67712.22720.02210.3856-0.182-0.0078-0.21950.1955-0.0898-0.28760.19740.02680.0011-0.03470.1149-0.02290.085739.410398.7846.8594
35.0642-2.25670.69285.16381.08436.15280.00960.4387-0.677-0.0498-0.14060.63760.5718-0.66750.1310.0627-0.06910.00510.2904-0.16150.217746.939983.8449-4.0194
42.8055-3.06-1.72945.16523.65964.4728-0.2679-0.0481-0.06240.58240.2713-0.21270.40950.2403-0.00350.08070.0119-0.03780.1012-0.04470.077152.584191.324910.864
54.6581-2.17810.0285.1124-0.86083.2635-0.1395-0.2596-0.01650.52320.0320.2075-0.0767-0.09130.10750.2287-0.00360.01770.1253-0.0530.115733.7484110.052842.5345
63.3478-3.25611.97465.6903-2.95152.6043-0.1895-0.4934-0.35840.43340.2990.52010.0723-0.2127-0.10950.32410.02840.12080.1701-0.03690.168923.4776112.247243.6533
73.82711.59260.55175.62491.07866.3141-0.0492-0.2352-0.50080.5556-0.24860.84610.4343-0.99650.29780.268-0.03290.19490.2625-0.12730.44626.7109118.841237.7999
84.1669-2.14952.3163.3968-0.95384.79940.03350.2986-0.08370.0936-0.19250.2681-0.058-0.0760.1590.15230.00530.06980.0764-0.08710.170320.434118.547828.0711
91.4905-0.19210.05812.66570.17284.1029-0.0647-0.2475-0.1950.2759-0.0652-0.20460.12130.10.12990.1474-0.0134-0.03190.10630.0410.137252.66689.758336.3538
101.9565-0.20660.99865.2719-0.90425.4117-0.1559-0.2175-0.18830.0350.16670.37920.1197-0.1972-0.01080.350.0257-0.07870.35460.16790.243253.473380.537955.1424
111.4860.43020.68747.41752.67223.7561-0.2602-0.5204-0.19970.76870.1460.990.1892-0.53130.11420.51760.07050.01650.55240.23780.384248.298676.149262.668
124.0082-0.478-6.24137.2064-3.386613.2554-0.5524-0.3722-0.31891.3740.32240.484-0.642-0.23550.230.7270.3368-0.02350.52350.16490.205147.891892.180953.627
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 73
2X-RAY DIFFRACTION2A74 - 197
3X-RAY DIFFRACTION3A198 - 256
4X-RAY DIFFRACTION4A257 - 310
5X-RAY DIFFRACTION5B2 - 106
6X-RAY DIFFRACTION6B107 - 156
7X-RAY DIFFRACTION7B157 - 248
8X-RAY DIFFRACTION8B249 - 309
9X-RAY DIFFRACTION9C3 - 132
10X-RAY DIFFRACTION10C133 - 183
11X-RAY DIFFRACTION11C184 - 272
12X-RAY DIFFRACTION12C273 - 308

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