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- PDB-1vl1: Crystal structure of 6-phosphogluconolactonase (TM1154) from Ther... -

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Basic information

Entry
Database: PDB / ID: 1vl1
TitleCrystal structure of 6-phosphogluconolactonase (TM1154) from Thermotoga maritima at 1.70A resolution
Components6-phosphogluconolactonase
KeywordsHYDROLASE / TM1154 / 6-PHOSPHOGLUCONOLACTONASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


6-phosphogluconolactonase / 6-phosphogluconolactonase activity / pentose-phosphate shunt / carbohydrate metabolic process
Similarity search - Function
6-Phosphogluconolactonase / 6-phosphogluconolactonase, DevB-type / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / Rossmann fold - #1360 / NagB/RpiA transferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 6-phosphogluconolactonase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of 6-phosphogluconolactonase (TM1154) from Thermotoga maritima at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0142
Polymers26,8221
Non-polymers1921
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.733, 75.146, 148.443
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-465-

HOH

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Components

#1: Protein 6-phosphogluconolactonase / 6PGL


Mass: 26821.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: PGL, DEVB, TM1154 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0N8, 6-phosphogluconolactonase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.93 Å3/Da / Density % sol: 35.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 0.2M (NH4)2HCitrate, 20% PEG-3350 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.000034
DetectorType: ADSC / Detector: CCD / Date: Apr 2, 2004
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000034 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 24729 / % possible obs: 79.46 % / Redundancy: 3.86 % / Biso Wilson estimate: 23.98 Å2 / Rsym value: 0.075 / Net I/σ(I): 16.59
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 2.57 % / Mean I/σ(I) obs: 2.93 / Num. unique all: 798 / Rsym value: 0.325 / % possible all: 26.04

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0001refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PBT

1pbt


Resolution: 1.55→37.11 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.158 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE NOMINAL RESOLUTION IS 1.70 A WITH 2581 OBSERVED REFLECTIONS BETWEEN 1.70 - 1.55 A (35 % COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.20395 1262 5.1 %RANDOM
Rwork0.16523 ---
obs0.16717 23466 79.32 %-
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: 22.367 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2--2.44 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 13 167 1946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221822
X-RAY DIFFRACTIONr_bond_other_d0.0010.021684
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9672470
X-RAY DIFFRACTIONr_angle_other_deg0.87633918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48423.6984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73315323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6941513
X-RAY DIFFRACTIONr_chiral_restr0.1150.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021991
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
X-RAY DIFFRACTIONr_nbd_refined0.2180.2335
X-RAY DIFFRACTIONr_nbd_other0.1840.21677
X-RAY DIFFRACTIONr_nbtor_other0.0830.21117
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3640.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.224
X-RAY DIFFRACTIONr_mcbond_it1.1511.51164
X-RAY DIFFRACTIONr_mcbond_other0.3271.5439
X-RAY DIFFRACTIONr_mcangle_it1.53521784
X-RAY DIFFRACTIONr_scbond_it2.7333798
X-RAY DIFFRACTIONr_scangle_it3.9794.5685
LS refinement shellResolution: 1.55→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 29 4.99 %
Rwork0.2 552 -
Refinement TLS params.Method: refined / Origin x: 4.1756 Å / Origin y: 21.4416 Å / Origin z: 17.9626 Å
111213212223313233
T-0.1261 Å2-0.001 Å20.0014 Å2--0.1382 Å20.0104 Å2---0.1137 Å2
L1.3461 °2-0.4957 °2-0.44 °2-1.4108 °20.4254 °2--2.3827 °2
S-0.0115 Å °-0.037 Å °-0.0406 Å °0.0799 Å °-0.0048 Å °-0.0085 Å °0.0308 Å °0.0398 Å °0.0163 Å °
Refinement TLS groupSelection: ALL

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