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- PDB-1zzg: Crystal structure of hypothetical protein TT0462 from Thermus the... -

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Basic information

Entry
Database: PDB / ID: 1zzg
TitleCrystal structure of hypothetical protein TT0462 from Thermus thermophilus HB8
Componentsglucose-6-phosphate isomerase
KeywordsISOMERASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm
Similarity search - Function
Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsYamamoto, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein TT0462 from Thermus thermophilus HB8
Authors: Yamamoto, H. / Kunishima, N.
History
DepositionJun 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glucose-6-phosphate isomerase
B: glucose-6-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)92,2822
Polymers92,2822
Non-polymers00
Water13,421745
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-62 kcal/mol
Surface area27860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.648, 131.950, 64.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-500-

HOH

21A-537-

HOH

31A-595-

HOH

DetailsThe biological assembly is a dimer in asymmetric unit.

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Components

#1: Protein glucose-6-phosphate isomerase / putative glucose-6-phosphate isomerase


Mass: 46141.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLL6, glucose-6-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.6
Details: PEG 4000, 2-propanol, TRIS, sodium citrate, sodium chloride, pH 5.6, MICROBATCH, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21031
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONSPring-8 BL26B121.071664
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS V1IMAGE PLATEMay 2, 2005MIRRORS
RIGAKU JUPITER 2102CCDMay 14, 2005MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MIRRORSSINGLE WAVELENGTHMx-ray1
2MIRRORSSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.0716641
ReflectionResolution: 1.9→40 Å / Num. all: 74413 / Num. obs: 74115 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.056 / Net I/σ(I): 19.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 3.57 / Num. unique all: 7258 / Rsym value: 0.522 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→10.54 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2449710.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.193 3454 5.1 %RANDOM
Rwork0.185 ---
all0.185 68183 --
obs0.185 67911 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.4743 Å2 / ksol: 0.388801 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.95→10.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6518 0 0 745 7263
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 528 4.7 %
Rwork0.264 10701 -
obs-11234 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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