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- PDB-3c5y: Crystal structure of a putative ribose 5-phosphate isomerase (sar... -

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Basic information

Entry
Database: PDB / ID: 3c5y
TitleCrystal structure of a putative ribose 5-phosphate isomerase (saro_3514) from novosphingobium aromaticivorans dsm at 1.81 A resolution
ComponentsRibose/galactose isomerase
KeywordsISOMERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


isomerase activity / carbohydrate metabolic process
Similarity search - Function
Ribose-5-phosphate isomerase, C-terminal / Ribose-5-phosphate isomerase / 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
NITRATE ION / Ribose/galactose isomerase
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative ribose 5-phosphate isomerase (YP_001165900.1) from Novosphingobium aromaticivorans DSM 12444 at 1.81 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Feb 1, 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
Revision 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribose/galactose isomerase
B: Ribose/galactose isomerase
C: Ribose/galactose isomerase
D: Ribose/galactose isomerase
E: Ribose/galactose isomerase
F: Ribose/galactose isomerase
G: Ribose/galactose isomerase
H: Ribose/galactose isomerase
I: Ribose/galactose isomerase
J: Ribose/galactose isomerase
K: Ribose/galactose isomerase
L: Ribose/galactose isomerase
M: Ribose/galactose isomerase
N: Ribose/galactose isomerase
O: Ribose/galactose isomerase
P: Ribose/galactose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)417,46585
Polymers413,18316
Non-polymers4,28269
Water47,8302655
1
A: Ribose/galactose isomerase
B: Ribose/galactose isomerase
C: Ribose/galactose isomerase
D: Ribose/galactose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,41322
Polymers103,2964
Non-polymers1,11718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
MethodPISA
2
E: Ribose/galactose isomerase
F: Ribose/galactose isomerase
G: Ribose/galactose isomerase
H: Ribose/galactose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,15734
Polymers103,2964
Non-polymers1,86230
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
MethodPISA
3
I: Ribose/galactose isomerase
J: Ribose/galactose isomerase
K: Ribose/galactose isomerase
L: Ribose/galactose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,04116
Polymers103,2964
Non-polymers74512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11090 Å2
MethodPISA
4
M: Ribose/galactose isomerase
N: Ribose/galactose isomerase
O: Ribose/galactose isomerase
P: Ribose/galactose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,85413
Polymers103,2964
Non-polymers5599
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.754, 109.462, 167.569
Angle α, β, γ (deg.)90.000, 102.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribose/galactose isomerase


Mass: 25823.945 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: YP_001165900.1, Saro_3514 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A4XEL3
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 61 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2655 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: NANODROP, 0.2M LiNO3, 20.0% PEG 3350, No Buffer pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 9, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91837 Å / Relative weight: 1
ReflectionResolution: 1.81→49.147 Å / Num. obs: 330786 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.954 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.69
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.81-1.870.4292.36916130758197.2
1.87-1.950.33237962835356197.2
1.95-2.040.2583.77535333522197.4
2.04-2.150.1825.17607333774197.6
2.15-2.280.1326.67203432025197.8
2.28-2.460.18.27625433855197.6
2.46-2.70.07710.27235532211197.6
2.7-3.090.05912.87478433275197.3
3.09-3.890.04216.57481233251197
3.89-49.1470.03818.87304532297192.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PPW

2ppw


Resolution: 1.81→49.147 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.189 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. EDO AND NO3 MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. RESIDUE 72 CYSTEIN IS OXIDIZED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 16707 5.1 %RANDOM
Rwork0.17 ---
obs0.173 330758 96.93 %-
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: 25.658 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20 Å20.77 Å2
2--0 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.81→49.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25574 0 276 2655 28505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02226612
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217956
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.98135887
X-RAY DIFFRACTIONr_angle_other_deg1.547343837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.77853505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67324.3331117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.616154518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.22415155
X-RAY DIFFRACTIONr_chiral_restr0.0950.24035
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0229967
X-RAY DIFFRACTIONr_gen_planes_other0.0030.025356
X-RAY DIFFRACTIONr_mcbond_it2.136316932
X-RAY DIFFRACTIONr_mcbond_other0.64337076
X-RAY DIFFRACTIONr_mcangle_it3.186526843
X-RAY DIFFRACTIONr_scbond_it5.50389680
X-RAY DIFFRACTIONr_scangle_it7.71118980
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 1263 -
Rwork0.255 23198 -
all-24461 -
obs--97.16 %

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