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- PDB-1vpv: Crystal structure of a degv lipid binding protein (tm1468) from t... -

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Basic information

Entry
Database: PDB / ID: 1vpv
TitleCrystal structure of a degv lipid binding protein (tm1468) from thermotoga maritima at 2.45 A resolution
ComponentsUPF0230 protein TM1468
KeywordsLIPID BINDING PROTEIN / Dak1/degv-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


Hypothetical Protein Tm841; Chain: A;domain 3 - #10 / Rossmann fold - #10170 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / Hypothetical Protein Tm841; Chain: A;domain 3 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / PHOSPHATE ION / Fatty acid-binding protein TM_1468
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of UPF0230 protein TM1468 (TM1468) from Thermotoga maritima at 2.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 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 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0230 protein TM1468
B: UPF0230 protein TM1468
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5266
Polymers68,8232
Non-polymers7034
Water1,928107
1
A: UPF0230 protein TM1468
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7633
Polymers34,4111
Non-polymers3512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UPF0230 protein TM1468
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7633
Polymers34,4111
Non-polymers3512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.256, 103.256, 115.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 1 - 284 / Label seq-ID: 13 - 296

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein UPF0230 protein TM1468


Mass: 34411.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1468 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1H9
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.42 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5
Details: 0.1M Cacodylate pH 6.5, 0.2M Mg(oAc)2, 27.5% PEG-8000, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97958
DetectorType: APS / Detector: CCD / Date: Apr 3, 2003
Details: sagitally focusing. 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.453→50 Å / Num. obs: 22755 / % possible obs: 96.36 % / Redundancy: 4.09 % / Biso Wilson estimate: 43.04 Å2 / Rsym value: 0.098 / Net I/σ(I): 13.77
Reflection shellResolution: 2.453→2.55 Å / Redundancy: 3.89 % / Mean I/σ(I) obs: 4.88 / Num. unique all: 2244 / Rsym value: 0.293 / % possible all: 97.78

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mgp

1mgp


Resolution: 2.45→47.16 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.889 / SU B: 13.876 / SU ML: 0.164 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.529 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PALMITIC ACID WAS PLACED BASED ON COMPARISON OF RELATED MODELS. NO DENSITY FOR RESIDUES A177-181 AND B177-185. VERY POOR DENSITY FOR A182-186.
RfactorNum. reflection% reflectionSelection details
Rfree0.25188 1174 5.2 %RANDOM
Rwork0.17987 ---
obs0.18355 21579 96.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.207 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.45→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4400 0 46 107 4553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224516
X-RAY DIFFRACTIONr_bond_other_d0.0010.024320
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.9996093
X-RAY DIFFRACTIONr_angle_other_deg0.845310047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0445556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62824.022184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94715834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6251531
X-RAY DIFFRACTIONr_chiral_restr0.0890.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02852
X-RAY DIFFRACTIONr_nbd_refined0.2130.2910
X-RAY DIFFRACTIONr_nbd_other0.190.24299
X-RAY DIFFRACTIONr_nbtor_other0.0880.22647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2149
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1930.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.23
X-RAY DIFFRACTIONr_mcbond_it2.26232864
X-RAY DIFFRACTIONr_mcbond_other0.58431133
X-RAY DIFFRACTIONr_mcangle_it2.85654533
X-RAY DIFFRACTIONr_scbond_it5.8281853
X-RAY DIFFRACTIONr_scangle_it8.135111560
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22195
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4208 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.310.5
medium thermal0.852
LS refinement shellResolution: 2.453→2.516 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 73 4.38 %
Rwork0.178 1593 -
obs--97.03 %
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)
11.89550.1524-0.69871.072-0.44691.64710.01140.06060.0856-0.1794-0.0414-0.0512-0.01220.0160.03-0.03020.0048-0.0101-0.1029-0.0429-0.0486-30.764-0.194-9.355
21.69140.5656-0.08191.5294-0.10620.62870.085-0.14470.00930.0901-0.06390.1380.0375-0.077-0.0211-0.0492-0.02070.0129-0.0176-0.0109-0.0506-55.18-31.34512.098
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 287 / Label seq-ID: 13 - 299

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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