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- PDB-1vmj: CRYSTAL STRUCTURE OF A PUTATIVE THIAMIN PHOSPHATE SYNTHASE (TM072... -

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Entry
Database: PDB / ID: 1vmj
TitleCRYSTAL STRUCTURE OF A PUTATIVE THIAMIN PHOSPHATE SYNTHASE (TM0723) FROM THERMOTOGA MARITIMA MSB8 AT 1.52 A RESOLUTION
Componentshypothetical protein TM0723
KeywordsTRANSFERASE / PUTATIVE THIAMIN PHOSPHATE SYNTHASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homologyYjbQ-like / Uncharacterised protein family UPF0047, YjbQ / YjbQ-like superfamily / Uncharacterised protein family UPF0047 / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (TM0723) from Thermotoga maritima at 1.52 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: hypothetical protein TM0723
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1295
Polymers17,8171
Non-polymers3114
Water3,837213
1
A: hypothetical protein TM0723
hetero molecules

A: hypothetical protein TM0723
hetero molecules

A: hypothetical protein TM0723
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,38615
Polymers53,4523
Non-polymers93412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8770 Å2
ΔGint-179 kcal/mol
Surface area15720 Å2
MethodPISA, PQS
2
A: hypothetical protein TM0723
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)108,77230
Polymers106,9056
Non-polymers1,86724
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_666-y+5/4,-x+5/4,-z+5/41
crystal symmetry operation19_666-x+5/4,-z+5/4,-y+5/41
crystal symmetry operation24_666-z+5/4,-y+5/4,-x+5/41
Buried area18420 Å2
ΔGint-395 kcal/mol
Surface area30550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.194, 110.194, 110.194
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-143-

SO4

21A-150-

HOH

31A-207-

HOH

41A-233-

HOH

51A-300-

HOH

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Components

#1: Protein hypothetical protein TM0723


Mass: 17817.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0723 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZI2
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.85 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6
Details: 3.2M (NH4)2SO4, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.024627
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2001 / Details: flat mirror
RadiationMonochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.024627 Å / Relative weight: 1
ReflectionResolution: 1.52→27.55 Å / Num. obs: 35764 / % possible obs: 100 % / Redundancy: 20.5 % / Biso Wilson estimate: 24.03 Å2 / Rsym value: 0.115 / Net I/σ(I): 19.2
Reflection shellResolution: 1.52→1.6 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 5117 / Rsym value: 0.01166 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
SCALA5.0)data scaling
MOLREPphasing
REFMAC5.2.0005refinement
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VMF

1vmf


Resolution: 1.52→27.55 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.965 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE DENSITY FOR SO4 4 IS LOCATED ON CRYSTALLOGRAPHIC 2-FOLD AXIS. THERE ARE SOME EXTRA DIFFERENCE DENSITY AFTER THE MODELLING OF 1/2 OCCUPIED SULFATE.
RfactorNum. reflection% reflectionSelection details
Rfree0.16302 1790 5 %RANDOM
Rwork0.144 ---
obs0.14495 33973 99.94 %-
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: 15.684 Å2
Refinement stepCycle: LAST / Resolution: 1.52→27.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1138 0 16 213 1367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221209
X-RAY DIFFRACTIONr_bond_other_d0.0020.021104
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9631630
X-RAY DIFFRACTIONr_angle_other_deg0.79532566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7175138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85823.22662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83615228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9071511
X-RAY DIFFRACTIONr_chiral_restr0.0840.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021302
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02254
X-RAY DIFFRACTIONr_nbd_refined0.240.2226
X-RAY DIFFRACTIONr_nbd_other0.1960.21121
X-RAY DIFFRACTIONr_nbtor_other0.0840.2729
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2161
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.223
X-RAY DIFFRACTIONr_mcbond_it1.4023696
X-RAY DIFFRACTIONr_mcbond_other0.4113283
X-RAY DIFFRACTIONr_mcangle_it2.27751134
X-RAY DIFFRACTIONr_scbond_it3.6748531
X-RAY DIFFRACTIONr_scangle_it5.3511496
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2575
X-RAY DIFFRACTIONr_metal_ion_refined0.2660.25
LS refinement shellResolution: 1.52→1.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 136 5.24 %
Rwork0.284 2460 -
obs--99.77 %
Refinement TLS params.Method: refined / Origin x: 48.981 Å / Origin y: 64.142 Å / Origin z: 50.498 Å
111213212223313233
T-0.0032 Å20.0021 Å2-0.018 Å2--0.0335 Å2-0.0058 Å2---0.0182 Å2
L0.5901 °20.1699 °20.2322 °2-0.3079 °20.1462 °2--0.5262 °2
S-0.0439 Å °-0.0317 Å °0.0728 Å °-0.0709 Å °0.0071 Å °0.0529 Å °-0.0954 Å °-0.0463 Å °0.0368 Å °
Refinement TLS groupSelection: ALL

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