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- PDB-1pbj: CBS domain protein -

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Basic information

Entry
Database: PDB / ID: 1pbj
TitleCBS domain protein
Componentshypothetical protein
KeywordsStructural genomics / unknown function / Methanothermobacter thermautotrophicus / CBS domain / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


: / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
CBS domain-containing protein
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus str. Delta H (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsCuff, M.E. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of a hypothetical protein from M. thermautotrophicus reveals a novel fold and a pseudo 2-fold axis of symmetry
Authors: Cuff, M.E. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMay 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2662
Polymers14,2421
Non-polymers241
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein
hetero molecules

A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5324
Polymers28,4832
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2980 Å2
ΔGint-46 kcal/mol
Surface area11770 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.788, 48.586, 56.481
Angle α, β, γ (deg.)90.00, 107.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein hypothetical protein


Mass: 14241.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Species: Methanothermobacter thermautotrophicus / Strain: delta H / Production host: Escherichia coli (E. coli) / References: UniProt: O27659
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 400, Hepes, MgCl2, NaCl, Imidazole, Glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97954, 0.97940, 0.95667
DetectorType: SBC-2 / Detector: CCD / Date: Apr 25, 2003
RadiationMonochromator: sagitally focused Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979541
20.97941
30.956671
ReflectionResolution: 1.4→17.93 Å / Num. all: 29950 / Num. obs: 27732 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.8 Å2 / Limit h max: 39 / Limit h min: -41 / Limit k max: 34 / Limit k min: -41 / Limit l max: 40 / Limit l min: 0 / Observed criterion F max: 724713.72 / Observed criterion F min: 4.4

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
d*TREKdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→17.93 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1389 5 %random
Rwork0.192 ---
all0.1924 29901 --
obs0.1924 27732 92.7 %-
Solvent computationSolvent model: Bulk solvent model / Bsol: 69.3617 Å2 / ksol: 0.396299 e/Å3
Displacement parametersBiso max: 65.69 Å2 / Biso mean: 21.78 Å2 / Biso min: 7.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20.56 Å2
2--1.54 Å20 Å2
3----2.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Luzzati d res high-1.4
Refinement stepCycle: LAST / Resolution: 1.4→17.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 1 297 1231
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg22.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.95
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.4-1.460.2691104.40.25323700.0263729248066.5
1.46-1.540.2241664.90.21931990.0173722336590.4
1.54-1.640.2272065.60.20434990.0163717370599.7
1.64-1.760.2211704.60.19635370.0173718370799.7
1.76-1.940.1841854.90.18835640.0143755374999.8
1.94-2.220.1771834.90.1835260.0133725370999.6
2.22-2.80.2041995.30.1835300.0143749372999.4
2.8-17.930.2031705.20.19631180.0163830328885.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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