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- PDB-1nri: Crystal Structure of Putative Phosphosugar Isomerase HI0754 from ... -

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Basic information

Entry
Database: PDB / ID: 1nri
TitleCrystal Structure of Putative Phosphosugar Isomerase HI0754 from Haemophilus influenzae
ComponentsHypothetical protein HI0754Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical Protein / Haemophilus influenzae / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


amino sugar catabolic process / N-acetylmuramic acid 6-phosphate etherase / N-acetylmuramic acid catabolic process / 1,6-anhydro-N-acetyl-beta-muramic acid catabolic process / ether hydrolase activity / carbon-oxygen lyase activity / peptidoglycan turnover / carbohydrate derivative binding / carbohydrate metabolic process
Similarity search - Function
N-acetylmuramic acid 6-phosphate etherase MurQ / C-terminal lid domain of glucokinase regulatory protein / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / Glucokinase regulatory protein family signature. / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 ...N-acetylmuramic acid 6-phosphate etherase MurQ / C-terminal lid domain of glucokinase regulatory protein / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / Glucokinase regulatory protein family signature. / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetylmuramic acid 6-phosphate etherase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsKim, Y. / Quartey, P. / Ng, R. / Zarembinski, T.I. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Hypothetical protein HI0754 from Haemophilus influenzae
Authors: Kim, Y. / Quartey, P. / Ng, R. / Zarembinski, T.I. / Joachimiak, A.
History
DepositionJan 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein HI0754


Theoretical massNumber of molelcules
Total (without water)33,2121
Polymers33,2121
Non-polymers00
Water3,531196
1
A: Hypothetical protein HI0754

A: Hypothetical protein HI0754


Theoretical massNumber of molelcules
Total (without water)66,4242
Polymers66,4242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7950 Å2
ΔGint-35 kcal/mol
Surface area17660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.656, 41.272, 77.252
Angle α, β, γ (deg.)90.00, 123.76, 90.00
Int Tables number5
Space group name H-MC121
Detailsdimer, the second part of the biological assembly is generated by the two fold axis: -x,y,1-z

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Components

#1: Protein Hypothetical protein HI0754 / Hypothesis


Mass: 33212.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI0754 / Production host: Escherichia coli (E. coli) / References: UniProt: P44862
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEGME 5000, Ammonium Sulfate,MES, EDTA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.9793
SYNCHROTRONAPS 19-ID20.97936, 0.97950, 0.94644
Detector
TypeIDDetectorDate
SBC-21CCDSep 13, 2001
SBC-22CCDMar 21, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2double crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.979361
30.97951
40.946441
ReflectionResolution: 1.88→43.5 Å / Num. all: 22432 / Num. obs: 22432 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.1
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 5 / Num. unique all: 2198 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CNS1refinement
d*TREKdata reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→43.5 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The N-term 11 residues and the C-terminal 47 residues were not built due to poor electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2101 9.9 %RANDOM
Rwork0.2116 ---
obs0.216 21252 96.9 %-
all-21252 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.9602 Å2 / ksol: 0.392679 e/Å3
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1--4.69 Å20 Å24.78 Å2
2---5.49 Å20 Å2
3---10.18 Å2
Refine analyzeLuzzati coordinate error free: 0.25 Å / Luzzati sigma a free: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1843 0 0 196 2039
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.822
X-RAY DIFFRACTIONc_scbond_it2.552
X-RAY DIFFRACTIONc_scangle_it3.412.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 352 10.5 %
Rwork0.229 3002 -
obs-2981 93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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