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

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Basic information

Entry
Database: PDB / ID: 2vko
TitleStructure of the soluble domain of the membrane protein TM1634 from Thermotoga maritima
ComponentsTM1634
KeywordsMEMBRANE PROTEIN / SAD / TPR MOTIF / THERMOTOGA MARITIMA / STRUCTURAL GENOMICS / JCSG / JOINT CENTER FOR 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: 1.79 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 20, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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

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Assembly

Deposited unit
A: TM1634
B: TM1634
C: TM1634
D: TM1634
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6896
Polymers49,2134
Non-polymers4772
Water3,819212
1
A: TM1634
C: TM1634
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8013
Polymers24,6062
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-24 kcal/mol
Surface area14280 Å2
MethodPQS
2
B: TM1634
D: TM1634
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8893
Polymers24,6062
Non-polymers2821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-24.8 kcal/mol
Surface area13910 Å2
MethodPQS
Unit cell
Length a, b, c (Å)50.852, 81.973, 68.327
Angle α, β, γ (deg.)90.00, 101.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TM1634


Mass: 12303.146 Da / Num. of mol.: 4 / Fragment: SOLUBLE DOMAIN, RESIDUES 27-128
Source method: isolated from a genetically manipulated source
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-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 54 % / Description: NONE
Crystal growpH: 5.5 / Details: 50% PEG200, 0.1 M NACITRATE PH 5.5

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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: 1.8→50 Å / Num. obs: 51063 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.9
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.57 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VKJ

2vkj


Resolution: 1.79→66.96 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.809 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAINS A AND C FORM THE BIOLOGICAL DIMER.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2595 5.1 %RANDOM
Rwork0.241 ---
obs0.243 48429 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20.53 Å2
2---0.26 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.79→66.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 32 212 3628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223444
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.312.0064573
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6985409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.15925.556162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00415722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4891512
X-RAY DIFFRACTIONr_chiral_restr0.1010.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022464
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.21799
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22396
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2223
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.2140
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.33922091
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.51453238
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.3181514
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.553111335
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: 1.79→1.84 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.401 192
Rwork0.288 3489
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)
13.50590.58380.2783.98462.93156.51880.2135-0.40980.0544-0.3110.0998-0.1771-0.13930.1437-0.3134-0.1548-0.03860.00960.0518-0.1725-0.0014-13.12932.9892-5.4511
23.2291-0.2534-1.22052.7363-0.45522.60610.0809-0.03530.0599-0.0749-0.0424-0.28090.08490.1635-0.0385-0.08780.0114-0.0252-0.0981-0.01550.0011-1.5364-6.3561-28.4217
33.9843-0.456-1.96452.11041.87665.9636-0.01160.406-0.29220.1695-0.06110.04470.0636-0.13890.0727-0.1201-0.01790.0320.0011-0.15730.0242-24.9364-0.9656-58.728
41.9957-1.70710.47642.5181-0.56361.4476-0.2988-0.02420.08260.31790.15-0.1575-0.22660.03520.1488-0.00860.0088-0.0031-0.07650.0083-0.029-13.201910.8026-37.1583
53.6147-0.2392-1.87261.51171.68538.131-0.0127-0.40470.21-0.0421-0.11010.1244-0.0749-0.02920.1228-0.14160.00480.00370.0162-0.1155-0.0107-26.4588-4.0591-4.0317
62.1274-0.8822-1.26592.89971.15373.77310.02570.02590.1425-0.2614-0.0610.2585-0.1565-0.32390.0353-0.06490.0063-0.0619-0.06-0.018-0.0095-23.8111-8.4736-28.7854
73.5314-0.28371.66741.81992.54795.3868-0.0260.5253-0.42130.0446-0.09660.0593-0.0891-0.05020.1226-0.126-0.060.02440.0582-0.1285-0.027912.49636.1556-59.6171
82.00470.73190.25012.68591.02031.713-0.0869-0.0478-0.10320.2451-0.00310.12450.1164-0.12930.09-0.0279-0.01140.0367-0.0670.0111-0.064916.283313.0028-35.7446
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 62
2X-RAY DIFFRACTION2A68 - 129
3X-RAY DIFFRACTION3B27 - 62
4X-RAY DIFFRACTION4B68 - 128
5X-RAY DIFFRACTION5C27 - 62
6X-RAY DIFFRACTION6C68 - 128
7X-RAY DIFFRACTION7D28 - 62
8X-RAY DIFFRACTION8D69 - 127

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