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- PDB-4m8l: crystal structure of RpiA-R5P complex -

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Basic information

Entry
Database: PDB / ID: 4m8l
Titlecrystal structure of RpiA-R5P complex
ComponentsRibose-5-phosphate isomerase A
KeywordsISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


D-ribose metabolic process / ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch / cytosol
Similarity search - Function
Ribose-5-phosphate isomerase, type A, subgroup / Ribose 5-phosphate isomerase, type A / Ribose 5-phosphate isomerase A (phosphoriboisomerase A) / Rossmann fold - #1360 / ACT domain / NagB/RpiA transferase-like / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RIBULOSE-5-PHOSPHATE / FORMAMIDE / Ribose-5-phosphate isomerase A
Similarity search - Component
Biological speciesFrancisella tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsRostankowski, R. / Borek, D. / Orlikowska, M. / Nakka, C. / Grimshaw, S. / Otwinowski, Z. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: crystal structure of RpiA-R5P complex
Authors: Rostankowski, R. / Borek, D. / Orlikowska, M. / Nakka, C. / Grimshaw, S. / Otwinowski, Z. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Other
Revision 1.2Sep 20, 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: Ribose-5-phosphate isomerase A
B: Ribose-5-phosphate isomerase A
C: Ribose-5-phosphate isomerase A
D: Ribose-5-phosphate isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,92154
Polymers97,9774
Non-polymers2,94450
Water5,260292
1
A: Ribose-5-phosphate isomerase A
C: Ribose-5-phosphate isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,69132
Polymers48,9882
Non-polymers1,70230
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-15 kcal/mol
Surface area18720 Å2
MethodPISA
2
B: Ribose-5-phosphate isomerase A
D: Ribose-5-phosphate isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,23122
Polymers48,9882
Non-polymers1,24220
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-15 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.203, 151.958, 36.290
Angle α, β, γ (deg.)90.00, 93.98, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALAA8 - 2238 - 223
21VALVALBB8 - 2238 - 223
12VALVALAA8 - 2238 - 223
22VALVALCC8 - 2238 - 223
13VALVALAA7 - 2237 - 223
23VALVALDD7 - 2237 - 223
14LEULEUBB8 - 2248 - 224
24LEULEUCC8 - 2248 - 224
15VALVALBB8 - 2238 - 223
25VALVALDD8 - 2238 - 223
16VALVALCC8 - 2238 - 223
26VALVALDD8 - 2238 - 223

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Ribose-5-phosphate isomerase A / Phosphoriboisomerase A / PRI


Mass: 24494.209 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: rpiA, FTW_1255 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: A4IYN5, ribose-5-phosphate isomerase
#2: Sugar
ChemComp-5RP / RIBULOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#3: Chemical...
ChemComp-ARF / FORMAMIDE


Type: L-peptide NH3 amino terminus / Mass: 45.041 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: CH3NO
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.22 M magnesium chloride 0.1M Tris pH 6.5, 21% (w/v) PEG 4000, additive: 40% formamide, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 34431 / % possible obs: 94.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 13.354
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 3.709 / Rsym value: 0.328 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KWM

3kwm


Resolution: 2.37→36.75 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.362 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.79 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27434 1728 5 %RANDOM
Rwork0.2375 ---
obs0.2394 32703 92.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.183 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20.09 Å2
2--0.97 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.37→36.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6650 0 184 292 7126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0196918
X-RAY DIFFRACTIONr_bond_other_d0.0020.026984
X-RAY DIFFRACTIONr_angle_refined_deg0.9991.9989308
X-RAY DIFFRACTIONr_angle_other_deg0.844316039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3735880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.92326.259270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.294151276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.5431525
X-RAY DIFFRACTIONr_chiral_restr0.0520.21140
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027852
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021582
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A139680.05
12B139680.05
21A139040.06
22C139040.06
31A136790.08
32D136790.08
41B138930.07
42C138930.07
51B135180.09
52D135180.09
61C136770.07
62D136770.07
LS refinement shellResolution: 2.37→2.428 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 114 -
Rwork0.266 2181 -
obs--83.45 %

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