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- PDB-1o22: Crystal structure of an orphan protein (TM0875) from Thermotoga m... -

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Basic information

Entry
Database: PDB / ID: 1o22
TitleCrystal structure of an orphan protein (TM0875) from Thermotoga maritima at 2.00 A resolution
Componentsorphan protein TM0875
KeywordsUNKNOWN FUNCTION / ORPHAN PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homologyOrphan Protein Tm0875; Chain: A; / Hypothetical protein TM0875 / Domain of unknown function DUF3855 / Hypothetical protein TM0875 / Domain of Unknown Function with PDB structure (DUF3855) / Alpha-Beta Complex / Alpha Beta / DUF3855 domain-containing protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of an orphan protein (TM0875) from Thermotoga maritima at 2.00-A resolution reveals a new fold.
Authors: Bakolitsa, C. / Schwarzenbacher, R. / McMullan, D. / Brinen, L.S. / Canaves, J.M. / Dai, X. / Deacon, A.M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, ...Authors: Bakolitsa, C. / Schwarzenbacher, R. / McMullan, D. / Brinen, L.S. / Canaves, J.M. / Dai, X. / Deacon, A.M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Jaroszewski, L. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Quijano, K. / Robb, A. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / von Delft, F. / Wang, X. / West, B. / Wolf, G. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionFeb 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.7Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: orphan protein TM0875


Theoretical massNumber of molelcules
Total (without water)20,3431
Polymers20,3431
Non-polymers00
Water1,838102
1
A: orphan protein TM0875

A: orphan protein TM0875


Theoretical massNumber of molelcules
Total (without water)40,6872
Polymers40,6872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5150 Å2
ΔGint-38 kcal/mol
Surface area16200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.410, 58.410, 102.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein orphan protein TM0875


Mass: 20343.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0875 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZX8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 25.5 % PEG 4000; 0.085 M Tris pH 8.5; 0.17 M Na(Ac), 15 % Glycerol, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 8.50
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.9
2150 mM1dropNaCl
30.25 mMTCEP1drop
49.4 mg/mlprotein1drop
525.5 %PEG40001reservoir
60.085 MTris1reservoirpH8.5
70.17 Msodium acetate1reservoir
815 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97780, 0.91840, 0.97920
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Oct 13, 2002
RadiationMonochromator: DOUBLE-CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97781
20.91841
30.97921
ReflectionResolution: 2→32.159 Å / Num. obs: 12462 / % possible obs: 99 % / Redundancy: 11.8 % / Biso Wilson estimate: 36.49 Å2 / Rsym value: 0.061 / Net I/σ(I): 28.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.375 / % possible all: 90.9
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 32.16 Å / Num. measured all: 148070 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 90.9 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALAdata scaling
RESOLVEmodel building
SOLVEphasing
CNSrefinement
XFITdata reduction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.49 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.183 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE BIOLOGICAL UNIT APPEARS TO BE A DIMER THAT STRADDLES THE CRYSTALLOGRAPHIC 4-FOLD. TLS GROUPS WERE CHOSEN WITH REFERENCE TO THE DIMER. WEAK DENSITY BOTH BEFORE FIRST AND AFTER LAST ...Details: THE BIOLOGICAL UNIT APPEARS TO BE A DIMER THAT STRADDLES THE CRYSTALLOGRAPHIC 4-FOLD. TLS GROUPS WERE CHOSEN WITH REFERENCE TO THE DIMER. WEAK DENSITY BOTH BEFORE FIRST AND AFTER LAST RESIDUE SUGGESTS THE GENERAL POSITION OF MORE N- AND C-TERMINAL RESIDUES THAN MODELLED HERE. CNS_SOLVE 1.1/CNS/XFIT/CCP4/TLS WERE ALSO USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 887 7.1 %RANDOM
Rwork0.182 ---
obs0.186 11574 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 0 102 1325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221272
X-RAY DIFFRACTIONr_bond_other_d0.0020.021144
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9781714
X-RAY DIFFRACTIONr_angle_other_deg0.82532697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3195148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.91425.90261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38115247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.177152
X-RAY DIFFRACTIONr_chiral_restr0.0980.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02246
X-RAY DIFFRACTIONr_nbd_refined0.1930.2181
X-RAY DIFFRACTIONr_nbd_other0.2430.21168
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.2775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it23743
X-RAY DIFFRACTIONr_mcangle_it3.70751210
X-RAY DIFFRACTIONr_scbond_it6.3428529
X-RAY DIFFRACTIONr_scangle_it9.51411504
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 52
Rwork0.233 757
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)
12.0478-1.92340.93162.852-0.79553.41850.0169-0.0610.06110.15070.0339-0.2103-0.04370.2542-0.0509-0.01620.00890.0113-0.0099-0.0099-0.053513.26412.20321.4161
22.18190.9926-0.04411.60480.28380.20080.0983-0.08490.0450.1843-0.09220.101-0.0135-0.0556-0.0061-0.0087-0.02150.0207-0.024-0.0072-0.0495-9.986810.16681.8026
31.46360.4615-1.03733.56573.77676.23970.1011-0.03880.16860.0836-0.04670.1373-0.16170.0153-0.0544-0.0336-0.02390.00930.0101-0.027-0.0203-14.963413.90631.0285
42.759-1.64360.95114.1545-2.24832.1293-0.131-0.3179-0.4976-0.01530.18140.17670.2977-0.2586-0.05040.0307-0.0310.03380.07850.01180.0963-18.6155-14.40043.4478
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA61 - 9573 - 107
2X-RAY DIFFRACTION2AA6 - 1418 - 26
3X-RAY DIFFRACTION2AA40 - 6052 - 72
4X-RAY DIFFRACTION2AA96 - 120108 - 132
5X-RAY DIFFRACTION2AA143 - 154155 - 166
6X-RAY DIFFRACTION3AA121 - 142133 - 154
7X-RAY DIFFRACTION4AA15 - 3927 - 51
Software
*PLUS
Name: REFMAC / Version: 5.1.995 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 32.16 Å / Num. reflection obs: 12461 / % reflection Rfree: 7.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.44
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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