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- PDB-1j5x: Crystal structure of Glucosamine-6-phosphate deaminase (TM0813) f... -

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Basic information

Entry
Database: PDB / ID: 1j5x
TitleCrystal structure of Glucosamine-6-phosphate deaminase (TM0813) from Thermotoga maritima at 1.8 A resolution
ComponentsGLUCOSAMINE-6-PHOSPHATE DEAMINASE
KeywordsHYDROLASE / STRUCTURAL GENOMICS / TM0813 / GLUCOSAMINE-6-PHOSPHATE DEAMINASE / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


carbohydrate derivative metabolic process / carbohydrate derivative binding
Similarity search - Function
GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / 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
SIS domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Glucosamine-6-phosphate deaminase (TM0813) from Thermotoga maritima at 1.8 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOSAMINE-6-PHOSPHATE DEAMINASE


Theoretical massNumber of molelcules
Total (without water)39,3031
Polymers39,3031
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: GLUCOSAMINE-6-PHOSPHATE DEAMINASE

A: GLUCOSAMINE-6-PHOSPHATE DEAMINASE


Theoretical massNumber of molelcules
Total (without water)78,6062
Polymers78,6062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area4680 Å2
ΔGint-24 kcal/mol
Surface area21840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.96, 72.96, 128.52
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

21A-401-

HOH

31A-485-

HOH

41A-617-

HOH

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Components

#1: Protein GLUCOSAMINE-6-PHOSPHATE DEAMINASE


Mass: 39302.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZS0, glucosamine-6-phosphate deaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / pH: 8
Details: 40% PEG-400, 0.1 M Imidazole pH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97980, 0.93218, 0.97999
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2001
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.932181
30.979991
ReflectionResolution: 1.7→45.054 Å / Num. obs: 39495 / % possible obs: 99.5 % / Redundancy: 18.3 % / Biso Wilson estimate: 23.99 Å2 / Rsym value: 0.07 / Net I/σ(I): 26.5
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.506 / % possible all: 95.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4data reduction
CCP4model building
SOLVEphasing
RESOLVEmodel building
CNS1refinement
CCP4(SCALA)data scaling
CCP4phasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: STANDARD CNS DICTIONARY/ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1914 4.8 %RANDOM
Rwork0.192 ---
obs0.192 37360 100 %-
all-37372 --
Solvent computationSolvent model: BULK SOLVENT CORRECTION / Bsol: 0.37 Å2 / ksol: 64.8 e/Å3
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.173 Å2-1.479 Å20 Å2
2---4.173 Å20 Å2
3---8.345 Å2
Refine analyzeLuzzati coordinate error obs: 0.216 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 0 294 2811
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.021
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_deg1.94
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.9351.5
X-RAY DIFFRACTIONc_mcangle_it2.5122
X-RAY DIFFRACTIONc_scbond_it3.2242
X-RAY DIFFRACTIONc_scangle_it4.1412.5
LS refinement shellResolution: 1.8→1.82 Å / Total num. of bins used: 38
RfactorNum. reflection% reflection
Rfree0.2985 47 4.9 %
Rwork0.2432 912 -

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