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- PDB-2raq: Crystal structure of the MTH889 protein from Methanothermobacter ... -

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Basic information

Entry
Database: PDB / ID: 2raq
TitleCrystal structure of the MTH889 protein from Methanothermobacter thermautotrophicus. Northeast Structural Genomics Consortium target TT205
ComponentsConserved protein MTH889
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyMTH889-like domain / Protein of unknown function DUF211 / MTH889-like domain superfamily / Uncharacterized ArCR, COG1888 / Alpha-Beta Plaits / 2-Layer Sandwich / metal ion binding / Alpha Beta / Conserved protein
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.11 Å
AuthorsForouhar, F. / Su, M. / Xu, X. / Seetharaman, J. / Mao, L. / Xiao, R. / Ma, L.-C. / Conover, K. / Baran, M.C. / Acton, T.B. ...Forouhar, F. / Su, M. / Xu, X. / Seetharaman, J. / Mao, L. / Xiao, R. / Ma, L.-C. / Conover, K. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Arrowsmith, C.H. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the MTH889 protein from Methanothermobacter thermautotrophicus.
Authors: Forouhar, F. / Su, M. / Xu, X. / Seetharaman, J. / Mao, L. / Xiao, R. / Ma, L.-C. / Conover, K. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Arrowsmith, C.H. / Hunt, J.F. / Tong, L.
History
DepositionSep 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE A 25-AA N-TERMINAL TAG WAS CLEAVED BY THROMBIN. IN RESULT, THE FINAL PURIFIED PROTEIN HAD ... SEQUENCE A 25-AA N-TERMINAL TAG WAS CLEAVED BY THROMBIN. IN RESULT, THE FINAL PURIFIED PROTEIN HAD ONLY MODIFICATION FOR ITS METHIONINE RESIDUES TO SE-MET RESIDUES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved protein MTH889
B: Conserved protein MTH889
C: Conserved protein MTH889
D: Conserved protein MTH889
E: Conserved protein MTH889
F: Conserved protein MTH889
G: Conserved protein MTH889
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,30221
Polymers76,7417
Non-polymers56114
Water97354
1
A: Conserved protein MTH889
B: Conserved protein MTH889
C: Conserved protein MTH889
D: Conserved protein MTH889
E: Conserved protein MTH889
F: Conserved protein MTH889
G: Conserved protein MTH889
hetero molecules

A: Conserved protein MTH889
B: Conserved protein MTH889
C: Conserved protein MTH889
D: Conserved protein MTH889
E: Conserved protein MTH889
F: Conserved protein MTH889
G: Conserved protein MTH889
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,60442
Polymers153,48214
Non-polymers1,12228
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area38930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.569, 113.569, 114.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Details14-mer oligomer made of two heptameric rings that are mediated by many calcium ions.

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Components

#1: Protein
Conserved protein MTH889


Mass: 10962.974 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H / Gene: MTH889 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold magic / References: UniProt: O26975
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 7.5
Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM DTT. Reservoir solution: 100 mM HEPES pH 7.5, 18% PEG 400, 200 mM CaCl2, 3% 1,6-Hexanediol, MICROBATCH UNDER OIL, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2007 / Details: mirrors
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: 3.1→80.58 Å / Num. all: 25673 / Num. obs: 25673 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.085 / Rsym value: 0.068 / Net I/σ(I): 26.13
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 6.13 / Num. unique all: 2573 / Rsym value: 0.282 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.11→80.58 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.862 / SU B: 43.319 / SU ML: 0.386 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.553 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Program CNS_1.2 has also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2802 691 4.9 %RANDOM
Rwork0.21559 ---
all0.22 25802 --
obs0.21871 13283 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.914 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3.11→80.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5082 0 14 54 5150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225152
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.9796989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9795645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.67825.625224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.82915960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3431528
X-RAY DIFFRACTIONr_chiral_restr0.1260.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023777
X-RAY DIFFRACTIONr_nbd_refined0.2890.22730
X-RAY DIFFRACTIONr_nbtor_refined0.3360.23510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2222
X-RAY DIFFRACTIONr_metal_ion_refined0.1330.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2920.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.23
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1960.22
X-RAY DIFFRACTIONr_mcbond_it0.6941.53306
X-RAY DIFFRACTIONr_mcangle_it1.25525315
X-RAY DIFFRACTIONr_scbond_it2.25832008
X-RAY DIFFRACTIONr_scangle_it3.3494.51674
LS refinement shellResolution: 3.11→3.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 50 -
Rwork0.225 938 -
obs-938 98.02 %
Refinement TLS params.Method: refined / Origin x: 19.4402 Å / Origin y: 75.2137 Å / Origin z: -7.4043 Å
111213212223313233
T-0.1003 Å2-0.0445 Å20.0071 Å2--0.0905 Å2-0.0192 Å2---0.1372 Å2
L0.5902 °20.3815 °2-0.1039 °2-0.5738 °2-0.1203 °2--0.0658 °2
S-0.09 Å °0.0836 Å °-0.0714 Å °-0.079 Å °0.0839 Å °-0.0015 Å °0.0212 Å °-0.0681 Å °0.0061 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 953 - 95
2X-RAY DIFFRACTION1BB2 - 952 - 95
3X-RAY DIFFRACTION1CC3 - 953 - 95
4X-RAY DIFFRACTION1DD3 - 953 - 95
5X-RAY DIFFRACTION1EE3 - 953 - 95
6X-RAY DIFFRACTION1FF3 - 953 - 95
7X-RAY DIFFRACTION1GG3 - 953 - 95

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