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- PDB-1bhw: LOW TEMPERATURE MIDDLE RESOLUTION STRUCTURE OF XYLOSE ISOMERASE F... -

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Basic information

Entry
Database: PDB / ID: 1bhw
TitleLOW TEMPERATURE MIDDLE RESOLUTION STRUCTURE OF XYLOSE ISOMERASE FROM MASC DATA
ComponentsXYLOSE ISOMERASE
KeywordsISOMERASE / MASC / MULTIWAVELENGTH ANOMALOUS SOLVENT CONTRAST
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Xylose isomerase, actinobacteria / Xylose isomerase / Xylose isomerase family profile. / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
Biological speciesActinoplanes missouriensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, RIGID BODY REFINEMENT / Resolution: 4.1 Å
AuthorsRamin, M. / Shepard, W. / Fourme, R. / Kahn, R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Multiwavelength anomalous solvent contrast (MASC): derivation of envelope structure-factor amplitudes and comparison with model values.
Authors: Ramin, M. / Shepard, W. / Fourme, R. / Kahn, R.
#1: Journal: Proteins / Year: 1988
Title: Structural Analysis of the 2.8 A Model of Xylose Isomerase from Actinoplanes Missouriensis
Authors: Rey, F. / Jenkins, J. / Janin, J. / Lasters, I. / Alard, P. / Claessens, M. / Matthyssens, G. / Wodak, S.
History
DepositionJun 10, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XYLOSE ISOMERASE
B: XYLOSE ISOMERASE
C: XYLOSE ISOMERASE
D: XYLOSE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)173,5904
Polymers173,5904
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32180 Å2
ΔGint-113 kcal/mol
Surface area46780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.910, 141.910, 227.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
XYLOSE ISOMERASE


Mass: 43397.465 Da / Num. of mol.: 4 / Mutation: H220N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes missouriensis (bacteria) / Plasmid: PMA5-I / Production host: Escherichia coli (E. coli) / Strain (production host): K527 / References: UniProt: P12851, xylose isomerase

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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: 3.7 Å3/Da / Density % sol: 62.6 %
Crystal growDetails: PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 124 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.99
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 1995 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 4.12→105.4 Å / Num. obs: 19684 / % possible obs: 97.3 % / Observed criterion σ(I): 3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 17.3
Reflection shellResolution: 4.12→4.29 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.041 / Mean I/σ(I) obs: 16.1 / Rsym value: 0.041 / % possible all: 75
Reflection
*PLUS
Num. measured all: 110358

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
SCALAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, RIGID BODY REFINEMENT
Starting model: 1XIN

1xin


Resolution: 4.1→8 Å / Cross valid method: THROUGHOUT
Rfactor% reflectionSelection details
Rfree0.321 10 %RANDOM
Rwork0.315 --
obs0.315 --
Refinement stepCycle: LAST / Resolution: 4.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12248 0 0 0 12248

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