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- PDB-2g4j: Anomalous substructure of Glucose isomerase -

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Basic information

Entry
Database: PDB / ID: 2g4j
TitleAnomalous substructure of Glucose isomerase
ComponentsXylose isomerase
KeywordsIsomerase/Metal-binding protein / anomalous substructure of glucose isomerase / Isomerase-Metal-binding protein COMPLEX
Function / homology
Function and homology information


xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function
Xylose isomerase, actinobacteria / Xylose isomerase / Xylose isomerase family profile. / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsMueller-Dieckmann, C. / Weiss, M.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.
Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2524
Polymers43,1521
Non-polymers1003
Water4,288238
1
A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,00816
Polymers172,6084
Non-polymers39912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
Buried area32150 Å2
ΔGint-241 kcal/mol
Surface area45870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.020, 97.590, 102.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Xylose isomerase /


Mass: 43152.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.7 Å3/Da / Density % sol: 54.46 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 40124 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
CCP4(SCALA)data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.181 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17701 812 2 %RANDOM
Rwork0.152 ---
obs0.15253 39312 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.945 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å20 Å2
2--1.41 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3041 0 3 238 3282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213122
X-RAY DIFFRACTIONr_bond_other_d0.0020.022804
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.9514227
X-RAY DIFFRACTIONr_angle_other_deg0.88236467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0835387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.622.941170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10915493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1891536
X-RAY DIFFRACTIONr_chiral_restr0.1060.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023598
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02712
X-RAY DIFFRACTIONr_nbd_refined0.230.2694
X-RAY DIFFRACTIONr_nbd_other0.1910.22742
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21556
X-RAY DIFFRACTIONr_nbtor_other0.0860.21728
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2200
X-RAY DIFFRACTIONr_metal_ion_refined0.2370.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3310.2158
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.219
X-RAY DIFFRACTIONr_mcbond_it1.2851.51975
X-RAY DIFFRACTIONr_mcbond_other0.3421.5792
X-RAY DIFFRACTIONr_mcangle_it1.8892.53039
X-RAY DIFFRACTIONr_scbond_it4.28951304
X-RAY DIFFRACTIONr_scangle_it6.207101187
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 46 -
Rwork0.249 2831 -
obs--98.19 %
Refinement TLS params.Method: refined / Origin x: -15.5572 Å / Origin y: -10.3225 Å / Origin z: -40.6428 Å
111213212223313233
T-0.093 Å2-0.0163 Å20.0212 Å2--0.0467 Å2-0.0041 Å2---0.0748 Å2
L0.34 °2-0.0168 °20.0702 °2-0.471 °20.0763 °2--0.4772 °2
S-0.0047 Å °-0.0255 Å °-0.0472 Å °0.0226 Å °-0.0169 Å °0.0354 Å °0.0544 Å °-0.0426 Å °0.0217 Å °

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