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- PDB-3q98: Structure of ygeW encoded protein from E. coli -

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Basic information

Entry
Database: PDB / ID: 3q98
TitleStructure of ygeW encoded protein from E. coli
Componentstranscarbamylase
KeywordsTRANSFERASE / Rossmann Fold / Unknown transcarbamylase
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / carboxyl- or carbamoyltransferase activity / ornithine carbamoyltransferase activity / arginine biosynthetic process via ornithine / citrulline biosynthetic process / amino acid metabolic process / amino acid binding
Similarity search - Function
Putative carbamoyltransferase YgeW / Aspartate/ornithine carbamoyltransferase / 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
Uncharacterized protein / Putative carbamoyltransferase YgeW
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 Å
AuthorsLi, Y. / Jing, Z. / Yu, X. / Allewell, N.M. / Tuchman, M. / Shi, D.
CitationJournal: Proteins / Year: 2011
Title: The ygeW encoded protein from Escherichia coli is a knotted ancestral catabolic transcarbamylase.
Authors: Li, Y. / Jin, Z. / Yu, X. / Allewell, N.M. / Tuchman, M. / Shi, D.
History
DepositionJan 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Jun 6, 2018Group: Data collection / Refinement description / Category: software / Item: _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: transcarbamylase


Theoretical massNumber of molelcules
Total (without water)45,2281
Polymers45,2281
Non-polymers00
Water2,666148
1
A: transcarbamylase

A: transcarbamylase

A: transcarbamylase


Theoretical massNumber of molelcules
Total (without water)135,6843
Polymers135,6843
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area8280 Å2
ΔGint-38 kcal/mol
Surface area42940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.250, 78.250, 100.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein transcarbamylase


Mass: 45228.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ygeW / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1R7G1, UniProt: Q46803*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 1.96 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 200 mM MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97933 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 13, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 23528 / Num. obs: 23411 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 5.8 / Num. unique all: 1686 / % possible all: 96.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
SHELXmodel building
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.001→28.067 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8505 / SU ML: 0.23 / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 3888 8.55 %RANDOM
Rwork0.1748 ---
all0.1799 49384 --
obs0.1791 22790 98.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.562 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 232.16 Å2 / Biso mean: 35.5349 Å2 / Biso min: 12.15 Å2
Baniso -1Baniso -2Baniso -3
1--3.6883 Å20 Å20 Å2
2---3.6883 Å20 Å2
3---7.3766 Å2
Refinement stepCycle: LAST / Resolution: 2.001→28.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2993 0 0 148 3141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073049
X-RAY DIFFRACTIONf_angle_d1.0564115
X-RAY DIFFRACTIONf_chiral_restr0.072454
X-RAY DIFFRACTIONf_plane_restr0.005530
X-RAY DIFFRACTIONf_dihedral_angle_d16.5011126
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 (%)
2.0007-2.07220.2393910.20243989438095
2.0722-2.15520.2253830.18454152453598
2.1552-2.25320.24493810.18134161454298
2.2532-2.3720.24813950.17794193458898
2.372-2.52050.24263840.18394146453098
2.5205-2.71490.24583950.17994183457899
2.7149-2.98790.27693890.19034181457099
2.9879-3.41960.21443940.18154190458499
3.4196-4.30580.18863830.14674202458599
4.3058-28.06970.21273930.174211460499
Refinement TLS params.Method: refined / Origin x: 23.0719 Å / Origin y: 49.4722 Å / Origin z: 46.1146 Å
111213212223313233
T0.1303 Å2-0.017 Å2-0.007 Å2-0.124 Å20.001 Å2--0.1266 Å2
L1.6904 °2-0.0909 °2-0.3883 °2-1.0475 °20.2113 °2--0.8804 °2
S0.0619 Å °0.1222 Å °0.0639 Å °-0.128 Å °-0.0202 Å °-0.1455 Å °-0.0594 Å °0.0453 Å °-0.0424 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 396
2X-RAY DIFFRACTION1allA1 - 544

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