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- PDB-1vk8: CRYSTAL STRUCTURE OF A PUTATIVE THIAMINE BIOSYNTHESIS/SALVAGE PRO... -

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Basic information

Entry
Database: PDB / ID: 1vk8
TitleCRYSTAL STRUCTURE OF A PUTATIVE THIAMINE BIOSYNTHESIS/SALVAGE PROTEIN (TM0486) FROM THERMOTOGA MARITIMA AT 1.80 A RESOLUTION
Componentshypothetical protein TM0486
KeywordsBIOSYNTHETIC PROTEIN / PROTEIN WITH POSSIBLE ROLE IN CELL WALL BIOGENESIS / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


Thiamine-binding protein / : / Thiamine-binding protein / Alpha-Beta Plaits - #930 / MTH1187/YkoF-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Thiamine-binding protein domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: TM0486 from the hyperthermophilic anaerobe Thermotoga maritima is a thiamin-binding protein involved in response of the cell to oxidative conditions.
Authors: Dermoun, Z. / Foulon, A. / Miller, M.D. / Harrington, D.J. / Deacon, A.M. / Sebban-Kreuzer, C. / Roche, P. / Lafitte, D. / Bornet, O. / Wilson, I.A. / Dolla, A.
History
DepositionMay 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 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_conn ...database_2 / 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein TM0486
B: hypothetical protein TM0486
C: hypothetical protein TM0486
D: hypothetical protein TM0486


Theoretical massNumber of molelcules
Total (without water)49,6958
Polymers49,6954
Non-polymers04
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
ΔGint-29 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.646, 47.650, 49.608
Angle α, β, γ (deg.)73.80, 62.90, 73.62
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
hypothetical protein TM0486


Mass: 12423.776 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: protein with possible role in cell wall biogenesis / Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0486 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYV6
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 36.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 9.6
Details: 20% PEG-8000, 0.1M CHES pH 9.5, pH 9.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K. cryo condition: 12% PEG 200.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0332, 0.9796
DetectorType: ADSC / Detector: CCD / Date: Dec 13, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.97961
ReflectionResolution: 1.8→41.71 Å / Num. obs: 25897 / % possible obs: 76.1 % / Redundancy: 1.9 % / Biso Wilson estimate: 24.97 Å2 / Rsym value: 0.06 / Net I/σ(I): 10.2
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 607 / Rsym value: 0.116 / % possible all: 23.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→41.71 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.867 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.142
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2). AN UNKNOWN LIGAND IS ASSOCIATED WITH EACH OF THE 4 SUBUNITS. UNAMBIGUOUS ASSIGNMENT OF THE IDENTITY OF THIS MOIETY WAS NOT POSSIBLE, ...Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2). AN UNKNOWN LIGAND IS ASSOCIATED WITH EACH OF THE 4 SUBUNITS. UNAMBIGUOUS ASSIGNMENT OF THE IDENTITY OF THIS MOIETY WAS NOT POSSIBLE, THOUGH THE DENSITY CAN BE CLOSELY ACCOUNTED FOR BY A GUANINE BASE. IT IS LABELED 'UNL' AND ALL ATOMS WERE REFINED AS OXYGEN ATOMS. BUMP RESTRAINTS WERE REMOVED FOR THE REFINEMENT OF ATOMS IN EACH OF THESE LIGANDS. 3). TLS GROUPS WERE CHOSEN BY PROTEIN SUBUNIT IDENTIFICATION IN THE CRYSTALLOGRAPHIC ASSYMETRIC UNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.18956 1336 5.2 %RANDOM
Rwork0.14151 ---
obs0.14404 24544 76.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.411 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.52 Å20.44 Å2
2--0.49 Å2-0.03 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 48 353 3415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223085
X-RAY DIFFRACTIONr_bond_other_d0.0020.022905
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.974142
X-RAY DIFFRACTIONr_angle_other_deg1.04736768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8115369
X-RAY DIFFRACTIONr_chiral_restr0.0790.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023344
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02618
X-RAY DIFFRACTIONr_nbd_refined0.3970.2739
X-RAY DIFFRACTIONr_nbd_other0.2490.23518
X-RAY DIFFRACTIONr_nbtor_other0.0870.21973
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.224
X-RAY DIFFRACTIONr_mcbond_it1.73731854
X-RAY DIFFRACTIONr_mcangle_it3.30153015
X-RAY DIFFRACTIONr_scbond_it5.71981231
X-RAY DIFFRACTIONr_scangle_it8.941111127
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 32 5.28 %
Rwork0.172 574 -
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)
11.07180.5391-0.32861.9619-0.15670.97-0.02530.0908-0.0445-0.05110.04840.06880.0392-0.0348-0.02320.02610.0034-0.00650.0211-0.00380.009521.21215.33438.529
22.14090.4341-0.37571.0041-0.22020.80990.0623-0.01760.01290.0865-0.0375-0.0809-0.03430.0415-0.02480.0240.0096-0.01250.0287-0.00340.006634.71925.41145.774
32.21230.69430.57131.41980.86530.80470.0784-0.07040.04610.14-0.08010.15080.1066-0.05790.00170.03020.00420.02070.0311-0.00250.028810.02430.27145.64
41.32220.84070.62282.07760.60550.735-0.01950.13280.083-0.00870.03180.0253-0.04780.0529-0.01230.01950.00320.0020.0290.0140.020923.64840.31938.433
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 9414 - 106
22BB2 - 9414 - 106
33CC1 - 9413 - 106
44DD2 - 9414 - 106

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