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- PDB-3hhe: Crystal structure of ribose-5-phosphate isomerase A from Bartonel... -

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Basic information

Entry
Database: PDB / ID: 3hhe
TitleCrystal structure of ribose-5-phosphate isomerase A from Bartonella henselae
ComponentsRibose-5-phosphate isomerase A
KeywordsISOMERASE / NIAID / SSGCID / deCODE / SBRI / UW / Bartonella / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / : / Ribose-5-phosphate isomerase A
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of ribose-5-phosphate isomerase A from Bartonella henselae
Authors: Edwards, T.E. / Abendroth, J.A. / Staker, B.L. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionMay 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5277
Polymers54,9532
Non-polymers5745
Water2,630146
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-17.2 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.190, 79.584, 151.127
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 27476.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Expressed with an N-terminal hexahistidine tag and 3C cleavage site. Not cleaved prior to crystallization.
Source: (gene. exp.) Bartonella henselae (bacteria) / Strain: Houston-1 / Gene: rpiA, BH06410 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6G3V6, ribose-5-phosphate isomerase
#2: Sugar ChemComp-5RP / RIBULOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: JCSG+ sparse matrix screen condition D12, 40 mM KH2PO4, 16% PEG 8000, 20% Glycerol, 2.16 mg/mL Protein, crystal tracking ID 208597d12, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 22355 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.148 / Χ2: 1.031 / Net I/σ(I): 10.909
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.38 / Num. unique all: 2180 / Χ2: 0.771 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.65 Å42.56 Å
Translation2.65 Å42.56 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UJ5

1uj5


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.207 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.792 / SU B: 7.002 / SU ML: 0.173 / SU R Cruickshank DPI: 0.359 / SU Rfree: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.359 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1141 5.1 %RANDOM
Rwork0.205 ---
obs0.207 22301 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.72 Å2 / Biso mean: 32.847 Å2 / Biso min: 16.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20 Å2
2--0.58 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3469 0 31 146 3646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223564
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.994830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1455466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.28524.745137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.99215597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1061516
X-RAY DIFFRACTIONr_chiral_restr0.0860.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212642
X-RAY DIFFRACTIONr_mcbond_it0.6251.52307
X-RAY DIFFRACTIONr_mcangle_it1.21223682
X-RAY DIFFRACTIONr_scbond_it2.11531257
X-RAY DIFFRACTIONr_scangle_it3.6084.51147
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 81 -
Rwork0.244 1561 -
all-1642 -
obs--99.03 %

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