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- PDB-3clm: Crystal structure of transaldolase (YP_208650.1) from Neisseria g... -

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Basic information

Entry
Database: PDB / ID: 3clm
TitleCrystal structure of transaldolase (YP_208650.1) from Neisseria gonorrhoeae FA 1090 at 1.14 A resolution
ComponentsTransaldolase
KeywordsLYASE / YP_208650.1 / transaldolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Transferase
Function / homology
Function and homology information


transaldolase / transaldolase activity / pentose-phosphate shunt / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Transaldolase type 2 / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of transaldolase (YP_208650.1) from Neisseria gonorrhoeae FA 1090 at 1.14 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Jul 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.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 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 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,60114
Polymers37,7861
Non-polymers81413
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.140, 83.030, 89.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE CRYSTAL PACKING ANALYSIS SUPPORTED BY ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY LEADS TO THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein Transaldolase


Mass: 37786.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: FA 1090 / Gene: YP_208650.1, tal, NGO1610 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5F6E9, transaldolase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.0840.82TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. 1.74 ANGSTROM MAD DATA COLLECTED FROM A CRYSTAL IN SPACE GROUP C2 (C 1 2 1) WERE USED TO PHASE AND TRACE AN INITIAL MODEL. THIS MODEL WAS THEN USED FOR MOLECULAR REPLACEMENT AGAINST A CRYSTAL IN SPACE GROUP P212121 THAT DIFFRACTED TO 1.14 ANGSTROMS.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop6NANODROP, 0.20M (NH4)2SO4, 20.0% PEG 3350, No Buffer pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop6.5NANODROP, 0.16M Ca(OAc)2, 20.0% Glycerol, 14.4% PEG 8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.97916
SYNCHROTRONAPS 23-ID-D20.97953, 0.91840, 0.97939
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDNov 19, 2007Flat mirror (vertical focusing)
MARMOSAIC 300 mm CCD2CCDOct 26, 2007Adjustable focusing mirrors in K-B geometry
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) Double crystalSINGLE WAVELENGTHMx-ray1
2Si(111) Double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979161
20.979531
30.91841
40.979391
ReflectionResolution: 1.14→29.579 Å / Num. obs: 107548 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 6.167 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 10.68
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.14-1.180.3262.3487296001,244
1.18-1.230.2612.712436167091,271.2
1.23-1.280.2243.522269184691,292.6
1.28-1.350.1974.540394230531,299.7
1.35-1.440.1535.641919234691,299.6
1.44-1.550.1057.839452217601,299.6
1.55-1.70.07510.239334212871,299.6
1.7-1.950.0514.342257224451,299.3
1.95-2.450.0322142098218531,299.3
2.45-29.5790.02427.544050221451,298.8

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Processing

Software
NameVersionClassificationNB
SHELXL-97refinement
PHENIXrefinement
SHELXphasing
SHELXrefinement
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
PHASERphasing
MolProbity3beta29model building
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 1.14→29.579 Å / Num. parameters: 29682 / Num. restraintsaints: 121313 / Cross valid method: FREE R / Stereochemistry target values: ENGH AND HUBER
Details: 1. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.2%. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION ...Details: 1. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.2%. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3. 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. 4. 1,2-ETHANEDIOL MOLECULES, A SULFATE ION FROM THE CRYSTALLIZATION CONDITIONS AND A CHLORIDE ION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.161 5430 5.1 %RANDOM
Rwork0.13 ---
all0.131 107466 --
obs0.13 107466 94 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1975) 201-228
Displacement parametersBiso mean: 10.882 Å2
Refinement stepCycle: LAST / Resolution: 1.14→29.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2638 0 50 437 3125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.072
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.019
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.001
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.047
X-RAY DIFFRACTIONs_approx_iso_adps0.033

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