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- PDB-3cbn: Crystal structure of a conserved protein (MTH639) from Methanobac... -

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Basic information

Entry
Database: PDB / ID: 3cbn
TitleCrystal structure of a conserved protein (MTH639) from Methanobacterium thermoautotrophicum
ComponentsConserved protein MTH639
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / RP-A / 10241d / PSI-II / NYSGXRC / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homologymth639 domain like / Protein of unknown function DUF371 / Mth639-like domain superfamily / Domain of unknown function (DUF371) / Jelly Rolls / Sandwich / Mainly Beta / Conserved protein
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.63 Å
AuthorsSatyanarayana, L. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a conserved protein (MTH639) from Methanobacterium thermoautotrophicum.
Authors: Satyanarayana, L. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionFeb 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved protein MTH639


Theoretical massNumber of molelcules
Total (without water)17,2861
Polymers17,2861
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.559, 63.162, 32.182
Angle α, β, γ (deg.)90.00, 112.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Conserved protein MTH639


Mass: 17286.068 Da / Num. of mol.: 1 / Fragment: Residues 22-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H / Gene: MTH639 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-codon+RIL / References: UniProt: O26735
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 1.72 Å3/Da / Density % sol: 28.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20%(w/v) PEG 3350, 0.1M Bis-Tris buffer pH 5.5. 3%(w/v) 6-Aminohexanoic acid, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 15, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. all: 14179 / Num. obs: 14179 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 34.4
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.107 / Num. unique all: 1389 / % possible all: 94.3

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.63→29.8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 574 -RANDOM
Rwork0.213 ---
all0.219 14179 --
obs0.213 14122 96.5 %-
Displacement parametersBiso mean: 14.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.113 Å20 Å22.415 Å2
2---0.94 Å20 Å2
3---1.052 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.63→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 0 0 126 1262
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.4
X-RAY DIFFRACTIONc_angle_deg0.005
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 1.63→1.73 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.277 91 -
Rwork0.244 --
obs-2153 92.5 %

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