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- PDB-1vr8: Crystal structure of GTP binding regulator (TM1622) from Thermoto... -

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Basic information

Entry
Database: PDB / ID: 1vr8
TitleCrystal structure of GTP binding regulator (TM1622) from Thermotoga Maritima at 1.75 A resolution
ComponentsGTP binding regulator
KeywordsSIGNALING PROTEIN / TM1622 / GTP BINDING REGULATOR / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homologyTM1622-like / Protein of unknown function DUF3242 / TM1622-like superfamily / Protein of unknown function (DUF3242) / Protein Transport Mog1p; Chain A / 3-Layer(aba) Sandwich / Alpha Beta / AZIDE ION / Uncharacterized protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of an ORFan protein (TM1622) from Thermotoga maritima at 1.75 A resolution reveals a fold similar to the Ran-binding protein Mog1p.
Authors: Xu, Q. / Krishna, S.S. / McMullan, D. / Schwarzenbacher, R. / Miller, M.D. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Astakhova, T. / Axelrod, H.L. / Canaves, J.M. / Carlton, D. / Chiu, H. ...Authors: Xu, Q. / Krishna, S.S. / McMullan, D. / Schwarzenbacher, R. / Miller, M.D. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Astakhova, T. / Axelrod, H.L. / Canaves, J.M. / Carlton, D. / Chiu, H.J. / Clayton, T. / DiDonato, M. / Duan, L. / Elsliger, M.A. / Feuerhelm, J. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Han, G.W. / Haugen, J. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Koesema, E. / Kreusch, A. / Kuhn, P. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Paulsen, J. / Quijano, K. / Reyes, R. / Rife, C.L. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / White, A. / Wolf, G. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionFeb 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
Remark 999SEQUENCE THE CONSTRUCT EXPRESSED COMPRISED AN N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHH] FOLLOWED ...SEQUENCE THE CONSTRUCT EXPRESSED COMPRISED AN N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHH] FOLLOWED BY RESIDUES 25-154 OF THE PREDICTED TM1622 GENE PRODUCT. IN ORDER TO REMOVE A PREDICTED TRANSMEMBRANE HELIX, THE FIRST 24 RESIDUES WERE NOT INCLUDED IN THE CONSTRUCT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP binding regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1586
Polymers16,7981
Non-polymers3605
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.730, 57.730, 87.944
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein GTP binding regulator


Mass: 16797.629 Da / Num. of mol.: 1 / Fragment: residues 25-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1622 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1V7
#2: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.32 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 277 K / pH: 6.5
Details: 12.0% PEG-20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99186, 0.97951, 0.97933
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 22, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.991861
20.979511
30.979331
ReflectionResolution: 1.75→29.31 Å / Num. obs: 16407 / % possible obs: 93.2 % / Redundancy: 4.4 % / Biso Wilson estimate: 25.41 Å2 / Rsym value: 0.068 / Net I/σ(I): 14.4
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1586 / Rsym value: 0.339 / % possible all: 63.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA5data scaling
SHELXDphasing
autoSHARPphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.75→29.31 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.433 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.096
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. LOOP 93-96 IS DISORDERED. THERE IS SOME EXTRA UNKNOWN DENSITY NEARBY WHICH IS NOT MODELED AS WELL.
RfactorNum. reflection% reflectionSelection details
Rfree0.18179 832 5.1 %RANDOM
Rwork0.1486 ---
obs0.15019 15549 93.16 %-
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: 23.241 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1098 0 24 172 1294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221160
X-RAY DIFFRACTIONr_bond_other_d0.0010.021054
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9311560
X-RAY DIFFRACTIONr_angle_other_deg0.73832433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6275135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44422.88552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46715197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.793156
X-RAY DIFFRACTIONr_chiral_restr0.090.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02250
X-RAY DIFFRACTIONr_nbd_refined0.1950.2201
X-RAY DIFFRACTIONr_nbd_other0.1710.21049
X-RAY DIFFRACTIONr_nbtor_other0.0850.2705
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.226
X-RAY DIFFRACTIONr_mcbond_it2.2993716
X-RAY DIFFRACTIONr_mcbond_other0.5543278
X-RAY DIFFRACTIONr_mcangle_it2.89751092
X-RAY DIFFRACTIONr_scbond_it3.1965562
X-RAY DIFFRACTIONr_scangle_it4.1925467
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2548
LS refinement shellResolution: 1.75→1.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 37 5.52 %
Rwork0.224 633 -
obs--53.09 %
Refinement TLS params.Method: refined / Origin x: 36.8774 Å / Origin y: -12.4241 Å / Origin z: -16.2932 Å
111213212223313233
T-0.167 Å20.0323 Å2-0.0125 Å2--0.1722 Å20.0026 Å2---0.1955 Å2
L1.0805 °20.1108 °20.1823 °2-3.3665 °20.0302 °2--1.2724 °2
S-0.0152 Å °0.0314 Å °0.0078 Å °-0.1138 Å °0.0238 Å °-0.0872 Å °0.0083 Å °0.046 Å °-0.0086 Å °
Refinement TLS groupSelection: ALL

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