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- PDB-1sq4: Crystal Structure of the Putative Glyoxylate Induced Protein from... -

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Basic information

Entry
Database: PDB / ID: 1sq4
TitleCrystal Structure of the Putative Glyoxylate Induced Protein from Pseudomonas aeruginosa, Northeast Structural Genomics Target PaR14
ComponentsGlyoxylate-induced Protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / double beta barrel protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


(S)-ureidoglycine aminohydrolase / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
THIOCYANATE ION / Uncharacterized protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsForouhar, F. / Chen, Y. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Putative Glyoxylate Induced Protein from Pseudomonas aeruginosa, Northeast Structural Genomics Target PaR14
Authors: Forouhar, F. / Chen, Y. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMar 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyoxylate-induced Protein
B: Glyoxylate-induced Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7536
Polymers64,5212
Non-polymers2324
Water1,60389
1
A: Glyoxylate-induced Protein
B: Glyoxylate-induced Protein
hetero molecules

A: Glyoxylate-induced Protein
B: Glyoxylate-induced Protein
hetero molecules

A: Glyoxylate-induced Protein
B: Glyoxylate-induced Protein
hetero molecules

A: Glyoxylate-induced Protein
B: Glyoxylate-induced Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,01324
Polymers258,0848
Non-polymers92916
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_655-y+3/2,x+1/2,z1
crystal symmetry operation4_465y-1/2,-x+3/2,z1
Buried area36120 Å2
ΔGint-209 kcal/mol
Surface area70870 Å2
MethodPISA
2
A: Glyoxylate-induced Protein
hetero molecules

A: Glyoxylate-induced Protein
hetero molecules

A: Glyoxylate-induced Protein
hetero molecules

A: Glyoxylate-induced Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,50712
Polymers129,0424
Non-polymers4658
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_655-y+3/2,x+1/2,z1
crystal symmetry operation4_465y-1/2,-x+3/2,z1
MethodPQS
3
B: Glyoxylate-induced Protein
hetero molecules

B: Glyoxylate-induced Protein
hetero molecules

B: Glyoxylate-induced Protein
hetero molecules

B: Glyoxylate-induced Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,50712
Polymers129,0424
Non-polymers4658
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_655-y+3/2,x+1/2,z1
crystal symmetry operation4_465y-1/2,-x+3/2,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.860, 106.860, 107.446
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Glyoxylate-induced Protein / GlxB


Mass: 32260.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: 878039 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9I4J5
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.53 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350 and 200mM potassium isothiocyanate, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→29.75 Å / Num. obs: 32679 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.8 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.101 / Net I/σ(I): 21.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 7.9 / Num. unique all: 3260 / Rsym value: 0.352 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.7→29.75 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3041 -Random
Rwork0.213 ---
all0.213 31279 --
obs0.262 31279 9.7 %-
Displacement parametersBiso mean: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å20 Å2
2---1.56 Å20 Å2
3---3.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4311 0 12 89 4412
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.2
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.324 543 -
Rwork0.263 --
obs-4293 11.2 %

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