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- PDB-2pmr: Crystal structure of a protein of unknown function from Methanoba... -

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Basic information

Entry
Database: PDB / ID: 2pmr
TitleCrystal structure of a protein of unknown function from Methanobacterium thermoautotrophicum
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyDomain of unknown function DUF357 / AF1782-like superfamily / Protein of unknown function (DUF357) / AF1782-like / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha / DUF357 domain-containing protein
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.32 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Wu, B. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a protein of unknown function from Methanobacterium thermoautotrophicum.
Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Wu, B. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionApr 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 24, 2012Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.6Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.7Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)10,3221
Polymers10,3221
Non-polymers00
Water1,18966
1
A: Uncharacterized protein

A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)20,6432
Polymers20,6432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2010 Å2
ΔGint-17 kcal/mol
Surface area8440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)37.370, 94.936, 46.258
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-146-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 10321.728 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H / Gene: MTH1690 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O27725
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7 / Details: 55% MPD, pH 7.0, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 14, 2007
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.32→47.468 Å / Num. all: 19764 / Num. obs: 19764 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 14.8
Reflection shellResolution: 1.32→1.39 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.439 / % possible all: 92.4

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.32→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.376 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1913 1014 5.1 %RANDOM
Rwork0.17459 ---
obs0.17545 19747 99.34 %-
all-19747 --
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: 17.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.32→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms626 0 0 66 692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022676
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.032.001914
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.109589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.09824.28635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82915147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.276156
X-RAY DIFFRACTIONr_chiral_restr0.0750.2103
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02499
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.2293
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2464
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.223
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8311.5415
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3372646
X-RAY DIFFRACTIONr_scbond_it2.2663292
X-RAY DIFFRACTIONr_scangle_it2.9244.5261
X-RAY DIFFRACTIONr_rigid_bond_restr1.5233707
X-RAY DIFFRACTIONr_sphericity_free2.001366
X-RAY DIFFRACTIONr_sphericity_bonded1.9273662
LS refinement shellResolution: 1.32→1.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 78 -
Rwork0.178 1260 -
obs--93.31 %

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