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- PDB-2vkj: Structure of the soluble domain of the membrane protein TM1634 fr... -

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Basic information

Entry
Database: PDB / ID: 2vkj
TitleStructure of the soluble domain of the membrane protein TM1634 from Thermotoga maritima
ComponentsTM1634
KeywordsMEMBRANE PROTEIN / TPR MOTIF JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / STRUCTURAL GENOMICS
Function / homologyMethane Monooxygenase Hydroxylase; Chain G, domain 1 - #2030 / TPR repeat profile. / Tetratricopeptide repeat / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / membrane / Uncharacterized protein
Function and homology information
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMcCleverty, C.J. / Columbus, L. / Kreusch, A. / Lesley, S.A. / Joint Center for Structural Genomics (JCSG)
CitationJournal: Protein Sci. / Year: 2008
Title: Structure and Ligand Binding of the Soluble Domain of a Thermotoga Maritima Membrane Protein of Unknown Function Tm1634.
Authors: Mccleverty, C.J. / Columbus, L. / Kreusch, A. / Lesley, S.A.
History
DepositionDec 19, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TM1634
B: TM1634
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8945
Polymers24,6062
Non-polymers2883
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-64.4 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.229, 76.199, 46.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein TM1634


Mass: 12303.146 Da / Num. of mol.: 2 / Fragment: SOLUBLE DOMAIN, RESIDUES 27-128
Source method: isolated from a genetically manipulated source
Details: ADDITIONAL RESIDUES GSHM AT N-TERMINUS / Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X1W9
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 6.5
Details: 30% PEG400, 0.2 M LI2SO4, 0.1 M NACACODYLATE, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 27259 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 29
Reflection shellResolution: 1.65→1.7 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.9 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→50.83 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.208 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAIN A AND CHAIN B SHOW DIFFERENT CONFORMATIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1453 5.1 %RANDOM
Rwork0.203 ---
obs0.205 27259 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å20 Å2
2---0.75 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 15 215 1956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221761
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3792.0012346
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.075210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34425.47684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71415366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.488156
X-RAY DIFFRACTIONr_chiral_restr0.1060.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021270
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2936
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21243
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2186
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0251.51056
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4821658
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9023769
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5924.5688
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.3 101
Rwork0.257 1708
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)
10.00160.0385-0.0380.9408-0.92682.28440.00560.0745-0.0307-0.01420.02570.06840.016-0.1917-0.0313-0.08990.00830.00620.01150.0051-0.010217.47433.29985.8121
20.1941-0.10020.21680.4615-0.00371.60190.01820.01640.0482-0.0115-0.0001-0.0495-0.13240.0651-0.0181-0.08110.02110.0216-0.02460.0027-0.007430.713915.90034.5457
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B24 - 49
2X-RAY DIFFRACTION1B50 - 64
3X-RAY DIFFRACTION1B65 - 90
4X-RAY DIFFRACTION1B91 - 106
5X-RAY DIFFRACTION1B107 - 129
6X-RAY DIFFRACTION2A24 - 49
7X-RAY DIFFRACTION2A50 - 64
8X-RAY DIFFRACTION2A65 - 90
9X-RAY DIFFRACTION2A91 - 106
10X-RAY DIFFRACTION2A107 - 129

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