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- PDB-1o5z: Crystal structure of Folylpolyglutamate synthase (TM0166) from Th... -

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Basic information

Entry
Database: PDB / ID: 1o5z
TitleCrystal structure of Folylpolyglutamate synthase (TM0166) from Thermotoga maritima at 2.10 A resolution
Componentsfolylpolyglutamate synthase/dihydrofolate synthase
KeywordsLIGASE / TM0166 / FOLYLPOLYGLUTAMATE SYNTHASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


dihydrofolate synthase activity / folic acid-containing compound biosynthetic process / tetrahydrofolylpolyglutamate synthase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Folylpolyglutamate synthase signature 2. / Folylpolyglutamate synthetase / Folylpolyglutamate synthase signature 1. / Folylpolyglutamate synthetase, conserved site / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central ...Folylpolyglutamate synthase signature 2. / Folylpolyglutamate synthetase / Folylpolyglutamate synthase signature 1. / Folylpolyglutamate synthetase, conserved site / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Folylpolyglutamate synthase/dihydrofolate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Folylpolyglutamate synthase (TM0166) from Thermotoga maritima at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jan 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 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN CONTINUOUS, NON-PROTEIN SURFACE DENSITY WAS MODELED AS RESIDUE UNL, OXYGENS IN AN UNKNOWN ...HETEROGEN CONTINUOUS, NON-PROTEIN SURFACE DENSITY WAS MODELED AS RESIDUE UNL, OXYGENS IN AN UNKNOWN LIGAND, 701-702.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: folylpolyglutamate synthase/dihydrofolate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8549
Polymers50,3991
Non-polymers4558
Water5,819323
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.751, 84.751, 280.679
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-903-

HOH

21A-920-

HOH

31A-1002-

HOH

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Components

#1: Protein folylpolyglutamate synthase/dihydrofolate synthase


Mass: 50399.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0166 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WY13
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.8 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.7
Details: 0.2 M Potassium Sulfate, 20% w/v/ PEG 3350, pH6.7, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Jun 25, 2003
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 33188 / Num. obs: 33188 / % possible obs: 100 % / Redundancy: 5.57 % / Biso Wilson estimate: 46.92 Å2 / Rsym value: 0.068 / Net I/σ(I): 22.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.86 % / Mean I/σ(I) obs: 2.57 / Num. unique all: 2163 / Rsym value: 0.511 / % possible all: 61.61

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Processing

Software
NameVersionClassification
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.9999refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fgs

1fgs


Resolution: 2.1→35.19 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / SU B: 13.953 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. SULFATE AND CHLORIDE WERE IN THE CRYSTALLIZATION AND PROTEIN BUFFERS RESPECTIVELY 3. A SEPARATE TLS GROUP WAS DEFINED FOR SULFATE 504 ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. SULFATE AND CHLORIDE WERE IN THE CRYSTALLIZATION AND PROTEIN BUFFERS RESPECTIVELY 3. A SEPARATE TLS GROUP WAS DEFINED FOR SULFATE 504 SINCE IT APPEARED DIRECTIONALLY DISORDERED. 4. CONTINUOUS, NON-PROTEIN SURFACE DENSITY WAS MODELED AS RESIDUE UNL, OXYGENS IN AN UNKNOWN LIGAND, 701-702. THESE ATOMS WERE ASSIGNED A V/D WAALS RADIUS OF ZERO DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.24421 1676 5.1 %RANDOM
Rwork0.18107 ---
obs0.1842 31388 92.1 %-
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: 42.889 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å2-0.78 Å20 Å2
2---1.56 Å20 Å2
3---2.34 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 31 323 3716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223437
X-RAY DIFFRACTIONr_bond_other_d0.0010.023204
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9724637
X-RAY DIFFRACTIONr_angle_other_deg0.87837447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6665418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63723.896154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.41915641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7191524
X-RAY DIFFRACTIONr_chiral_restr0.0940.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023735
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
X-RAY DIFFRACTIONr_nbd_refined0.2270.2831
X-RAY DIFFRACTIONr_nbd_other0.190.23634
X-RAY DIFFRACTIONr_nbtor_other0.0930.22261
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2248
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2870.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3120.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.290.220
X-RAY DIFFRACTIONr_mcbond_it0.9451.52243
X-RAY DIFFRACTIONr_mcangle_it1.34923384
X-RAY DIFFRACTIONr_scbond_it2.21531472
X-RAY DIFFRACTIONr_scangle_it3.4034.51253
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 80 5.11 %
Rwork0.286 1487 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.07270.02940.32231.664-0.75723.71480.1552-0.13270.06980.1467-0.03790.1315-0.23050.0812-0.1173-0.1893-0.03610.009-0.2511-0.0315-0.161130.96963.8689106.0164
25.53940.41950.52254.54373.16774.07820.1496-0.24960.4727-0.02470.0661-0.3336-0.29540.0307-0.2156-0.1497-0.0310.0315-0.1459-0.0945-0.122458.1688-0.9186108.5032
3514.6232-158.2912-200.8499565.705997.8641533.35220.4665-0.3681-0.94221.6884-0.5417-0.6157-0.46141.49090.07520.14750.05120.05980.1476-0.00110.157566.49473.704993.8952
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A

IDRefine TLS-IDLabel asym-IDAuth seq-IDLabel seq-ID
11A-2 - 29310 - 305
22A294 - 430306 - 442
33E504

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