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- PDB-4e3v: Crystal Structure of XYLOSE ISOMERASE FROM STREPTOMYCES RUBIGINOS... -

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Basic information

Entry
Database: PDB / ID: 4e3v
TitleCrystal Structure of XYLOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS Cryoprotected in Proline
ComponentsXylose isomerase
KeywordsISOMERASE
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / 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
: / PROLINE / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.503 Å
AuthorsTanner, J.J. / Pemberton, T.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Proline: Mother Nature's cryoprotectant applied to protein crystallography.
Authors: Pemberton, T.A. / Still, B.R. / Christensen, E.M. / Singh, H. / Srivastava, D. / Tanner, J.J.
History
DepositionMar 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_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

Downloads & links

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Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6706
Polymers43,2831
Non-polymers3865
Water5,837324
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)174,67924
Polymers173,1334
Non-polymers1,54620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area32220 Å2
ΔGint-279 kcal/mol
Surface area46010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.493, 98.022, 102.425
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-751-

HOH

21A-815-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase

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Non-polymers , 5 types, 329 molecules

#2: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.0M ammonium sulfate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→19.46 Å / Num. all: 72416 / Num. obs: 72416 / % possible obs: 99.6 %

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XIF

1xif


Resolution: 1.503→19.46 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.17 / σ(F): 1.35 / Phase error: 16.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1793 3657 5.05 %
Rwork0.1643 --
obs0.165 72403 97.72 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.605 Å2 / ksol: 0.404 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2973 Å2-0 Å20 Å2
2--1.7763 Å2-0 Å2
3----1.479 Å2
Refinement stepCycle: LAST / Resolution: 1.503→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 20 324 3345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063147
X-RAY DIFFRACTIONf_angle_d1.1074271
X-RAY DIFFRACTIONf_dihedral_angle_d12.3761166
X-RAY DIFFRACTIONf_chiral_restr0.07442
X-RAY DIFFRACTIONf_plane_restr0.006578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.503-1.52270.4327980.33871834X-RAY DIFFRACTION68
1.5227-1.54350.36221270.27872567X-RAY DIFFRACTION95
1.5435-1.56560.24081320.23992625X-RAY DIFFRACTION97
1.5656-1.58890.22661400.19022585X-RAY DIFFRACTION97
1.5889-1.61370.17691340.15972610X-RAY DIFFRACTION98
1.6137-1.64020.16511470.14022622X-RAY DIFFRACTION98
1.6402-1.66850.1811380.14452629X-RAY DIFFRACTION98
1.6685-1.69880.15961390.14052650X-RAY DIFFRACTION98
1.6988-1.73140.17171350.1432667X-RAY DIFFRACTION99
1.7314-1.76670.17741440.13922643X-RAY DIFFRACTION99
1.7667-1.80510.14581390.14432659X-RAY DIFFRACTION99
1.8051-1.84710.15721330.14732667X-RAY DIFFRACTION99
1.8471-1.89320.16411240.15332666X-RAY DIFFRACTION99
1.8932-1.94440.17971280.15072663X-RAY DIFFRACTION99
1.9444-2.00160.18761430.16282693X-RAY DIFFRACTION99
2.0016-2.06610.16471600.15612662X-RAY DIFFRACTION99
2.0661-2.13980.17361600.16922662X-RAY DIFFRACTION100
2.1398-2.22540.17361490.15882712X-RAY DIFFRACTION100
2.2254-2.32650.17531660.15512662X-RAY DIFFRACTION100
2.3265-2.4490.17521520.15862692X-RAY DIFFRACTION100
2.449-2.60210.20421470.16992701X-RAY DIFFRACTION100
2.6021-2.80240.19891270.17832750X-RAY DIFFRACTION100
2.8024-3.08350.1921550.17952716X-RAY DIFFRACTION100
3.0835-3.52730.181490.16832765X-RAY DIFFRACTION100
3.5273-4.43540.13871540.14062763X-RAY DIFFRACTION100
4.4354-19.460.16651370.16932881X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 30.7345 Å / Origin y: 38.8119 Å / Origin z: 61.723 Å
111213212223313233
T0.0437 Å2-0.008 Å20.0116 Å2-0.0601 Å2-0.0022 Å2--0.0536 Å2
L0.1713 °20.0342 °20.0254 °2-0.194 °2-0.0032 °2--0.2736 °2
S-0.0053 Å °-0.0253 Å °-0.0206 Å °0.0219 Å °-0.0095 Å °0.028 Å °0.0342 Å °-0.05 Å °0.0144 Å °
Refinement TLS groupSelection details: Chain A and resseq 3:387

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