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- PDB-1o1x: Crystal structure of a ribose 5-phosphate isomerase rpib (tm1080)... -

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Basic information

Entry
Database: PDB / ID: 1o1x
TitleCrystal structure of a ribose 5-phosphate isomerase rpib (tm1080) from thermotoga maritima at 1.90 A resolution
Componentsribose-5-phosphate isomerase RpiB
KeywordsISOMERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


D-allose catabolic process / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch / isomerase activity
Similarity search - Function
Ribose 5-phosphate isomerase B / Sugar-phosphate isomerase, RpiB/LacA/LacB family / Sugar-phosphate isomerase, RpiB/LacA/LacB superfamily / Ribose/Galactose Isomerase / Ribose 5-phosphate Isomerase B; Chain: A, / Sugar-phosphate isomerase, RpiB/LacA/LacB / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sugar-phosphate isomerase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a ribose-5-phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 A resolution.
Authors: Xu, Q. / Schwarzenbacher, R. / McMullan, D. / von Delft, F. / Brinen, L.S. / Canaves, J.M. / Dai, X. / Deacon, A.M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. / ...Authors: Xu, Q. / Schwarzenbacher, R. / McMullan, D. / von Delft, F. / Brinen, L.S. / Canaves, J.M. / Dai, X. / Deacon, A.M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Jaroszewski, L. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Levin, I. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Quijano, K. / Robb, A. / Spraggon, G. / Stevens, F. / van den Bedem, H. / Velasquez, J. / Vincent, J. / Wang, X. / West, B. / Wolf, G. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionFeb 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BIOLOGICAL UNIT IS A TETRAMER WITH 222 POINT SYMMETRY, FORMED BY CRYSTALLOGRAPHIC SYMMETRY, AS ADJUDGED BY EXTENSIVE HYDROPHOBIC CONTACTS BETWEEN THESE UNITS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ribose-5-phosphate isomerase RpiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6262
Polymers17,5071
Non-polymers1181
Water3,819212
1
A: ribose-5-phosphate isomerase RpiB
hetero molecules

A: ribose-5-phosphate isomerase RpiB
hetero molecules

A: ribose-5-phosphate isomerase RpiB
hetero molecules

A: ribose-5-phosphate isomerase RpiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5038
Polymers70,0304
Non-polymers4734
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area10130 Å2
ΔGint-91 kcal/mol
Surface area20690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.490, 73.890, 87.740
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 ribose-5-phosphate isomerase RpiB


Mass: 17507.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1080 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0G9, ribose-5-phosphate isomerase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.56 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 277 K / pH: 7
Details: 40 % (+/-)-2-Methyl-2,4-Pentanediol; 0.1 M HEPES pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, pH 7.00
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.9
2150 mM1dropNaCl
30.25 mMTCEP1drop
412 mg/mlprotein1drop
540 %MPD1reservoir
60.1 MHEPES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.91837, 0.97931, 0.97892
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 26, 2002
Details: FLAT MIRROR,SINGLE CRYSTAL SI(311) BENT MONOCHROMATOR
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979311
30.978921
ReflectionResolution: 1.9→29.788 Å / Num. obs: 15973 / % possible obs: 99.1 % / Redundancy: 4.7 % / Rsym value: 0.067 / Net I/σ(I): 15
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.284 / % possible all: 93.2
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 29.79 Å / Observed criterion σ(F): 0 / Num. measured all: 75731 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 93.2 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALAdata scaling
RESOLVEmodel building
SOLVEphasing
CNSrefinement
MOSFLMdata reduction
XFITdata reduction
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→28.26 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 4.442 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THERE IS WEAK DIFFERENCE DENSITY AT THE N-TERMINUS, APPARENTLY INDICATING AT LEAST ONE MORE HIS- TAG RESIDUE; IT WAS NOT MODELLED BECAUSE AT FULL OCCUPANCY, IT RESULTS IN A WORSE RFREE. ...Details: THERE IS WEAK DIFFERENCE DENSITY AT THE N-TERMINUS, APPARENTLY INDICATING AT LEAST ONE MORE HIS- TAG RESIDUE; IT WAS NOT MODELLED BECAUSE AT FULL OCCUPANCY, IT RESULTS IN A WORSE RFREE. SEVERAL LARGE BLOBS OF DIFFERENCE DENSITY THAT COULD NOT BE UNAMBIGUOUSLY IDENTIFIED, AND HAVE BEEN MODELLED AS CLOSELY-SPACED SOLVENT INSTEAD. THESE OCCUR NEAR THE FOLLOWING:A25, A51, A60, A82, A114, A127, A133. INITIAL REFINEMENT WAS PERFORMED USING CNS. REBUILDING WAS PERFORMED USING XFIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.138 803 5 %random
Rwork0.117 ---
obs0.118 15168 100 %-
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: 13.98 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20 Å2
2---1.1 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1139 0 8 212 1359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211199
X-RAY DIFFRACTIONr_bond_other_d0.0060.021122
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9631622
X-RAY DIFFRACTIONr_angle_other_deg0.93432603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5295144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57123.44858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57215215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7321510
X-RAY DIFFRACTIONr_chiral_restr0.10.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021314
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02247
X-RAY DIFFRACTIONr_nbd_refined0.2170.2220
X-RAY DIFFRACTIONr_nbd_other0.2390.21269
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.2702
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.2140
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3080.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7721.5724
X-RAY DIFFRACTIONr_mcangle_it1.46721167
X-RAY DIFFRACTIONr_scbond_it2.5623475
X-RAY DIFFRACTIONr_scangle_it4.2464.5455
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.19 60
Rwork0.213 1030
Refinement TLS params.Method: refined / Origin x: 22.905 Å / Origin y: 7.165 Å / Origin z: 29.085 Å
111213212223313233
T0.0047 Å20.0014 Å2-0.0128 Å2--0.0036 Å20.0144 Å2---0.0011 Å2
L1.1105 °2-0.1773 °2-0.2288 °2-0.8983 °20.083 °2--1.1127 °2
S-0.0173 Å °0.0099 Å °-0.0212 Å °-0.0314 Å °0.0247 Å °0.0693 Å °-0.0308 Å °-0.0846 Å °-0.0074 Å °
Software
*PLUS
Name: REFMAC / Version: 5.1.955 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 29.79 Å / Num. reflection all: 15971 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.52
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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