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- PDB-1vpq: CRYSTAL STRUCTURE OF a DUF72 family protein (TM1631) FROM THERMOT... -

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Entry
Database: PDB / ID: 1vpq
TitleCRYSTAL STRUCTURE OF a DUF72 family protein (TM1631) FROM THERMOTOGA MARITIMA MSB8 AT 2.20 A RESOLUTION
Componentshypothetical protein TM1631
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homologyProtein of unknown function UPF0759 / Protein of unknown function DUF72 / UPF0759 superfamily / Protein of unknown function DUF72 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (TM1631) from Thermotoga maritima at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein TM1631
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5184
Polymers33,2301
Non-polymers2883
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein TM1631
hetero molecules

A: hypothetical protein TM1631
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0368
Polymers66,4592
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area3060 Å2
ΔGint-115 kcal/mol
Surface area22050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.286, 136.238, 80.461
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-264-

SO4

21A-305-

HOH

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Components

#1: Protein hypothetical protein TM1631


Mass: 33229.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1631 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1W6
#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.: 91 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.244.02
22.2845.59DATA FROM A SE-MET CONTAINING CRYSTAL IN SPACEGROUP P32 WAS USED FOR THE MAD PHASING EXPERIMENTS AT 2.8 ANGSTROMS RESOLUTION. THIS MAD STRUCTURE WAS USED AS A MOLECULAR REPLACEMENT MODEL TO PHASE THE STRUCTURE AT A RESOLUTION OF 2.2 ANGSTROMS IN THE C222(1) SPACEGROUP.
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop9.51.26M (NH4)2SO4, 0.2M NaCl 0.1M CHES pH9.5 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop8.30.2M K3Citrate, 20.0% PEG-3350, No Buffer pH 8.3, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL11-111.033169
SYNCHROTRONAPS 19-BM20.98036, 0.98014, 0.96427
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDFeb 7, 2002flat mirror
APS 2CCDNov 15, 2003Rosenbaum-Rock vertical focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystal Si(311) bent monochromatorSINGLE WAVELENGTHMx-ray1
2Rosenbaum-Rock double-crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331691
20.980361
30.980141
40.964271
ReflectionResolution: 2.2→49.63 Å / Num. obs: 13378 / % possible obs: 88.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.5
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.8 / Num. unique all: 736 / % possible all: 67.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SHARPphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 2.2→49.63 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 18.974 / SU ML: 0.228 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.386 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1).HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2).A SO4 ANION IS LOCATED AT THE TWO-FOLD CRYSTALLOGRAPHIC SYMMETRY AXIS AT THE INTERFACE BETWEEN TWO MONOMERS. THE S AND O ATOMS ON ...Details: 1).HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2).A SO4 ANION IS LOCATED AT THE TWO-FOLD CRYSTALLOGRAPHIC SYMMETRY AXIS AT THE INTERFACE BETWEEN TWO MONOMERS. THE S AND O ATOMS ON THESE RESIDUES WERE MODELED WITH OCCUPANCIES OF 0.50.
RfactorNum. reflection% reflectionSelection details
Rfree0.26256 656 4.9 %RANDOM
Rwork0.20602 ---
obs0.20872 12722 87.61 %-
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: 29.804 Å2
Baniso -1Baniso -2Baniso -3
1-3.77 Å20 Å20 Å2
2---2.85 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 15 91 2286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222270
X-RAY DIFFRACTIONr_bond_other_d0.0050.021940
X-RAY DIFFRACTIONr_angle_refined_deg1.051.9443088
X-RAY DIFFRACTIONr_angle_other_deg0.73934493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8545259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37923.445119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15415353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7121511
X-RAY DIFFRACTIONr_chiral_restr0.060.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02531
X-RAY DIFFRACTIONr_nbd_refined0.1890.2433
X-RAY DIFFRACTIONr_nbd_other0.1860.21967
X-RAY DIFFRACTIONr_nbtor_other0.0820.21104
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1730.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3030.25
X-RAY DIFFRACTIONr_mcbond_it0.5261.51399
X-RAY DIFFRACTIONr_mcbond_other0.0541.5519
X-RAY DIFFRACTIONr_mcangle_it0.60422113
X-RAY DIFFRACTIONr_scbond_it0.89631107
X-RAY DIFFRACTIONr_scangle_it1.3024.5975
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21093
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 37 5.04 %
Rwork0.351 697 -
obs--66.91 %
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)
11.46891.22790.18536.25291.33993.0614-0.0194-0.291-0.03460.7462-0.09350.4829-0.274-0.3680.1129-0.01450.04150.03690.00310.03940.021116.85511.446.622
21.4059-0.14820.09873.1227-0.02211.7808-0.0036-0.149-0.05880.18980.02290.03430.0216-0.0318-0.0193-0.204900.0072-0.07130.0219-0.110326.01623.169-4.045
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 5913 - 71
2260 - 25972 - 271

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