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- PDB-1mjh: Structure-based assignment of the biochemical function of hypothe... -

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Basic information

Entry
Database: PDB / ID: 1mjh
TitleStructure-based assignment of the biochemical function of hypothetical protein MJ0577: A test case of structural genomics
ComponentsPROTEIN (ATP-BINDING DOMAIN OF PROTEIN MJ0577)
KeywordsHYPOTHETICAL PROTEIN / STRUCTURAL GENOMICS / FUNCTIONAL ASSIGNMENT / ATP BINDING PROTEIN / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


ATP binding / cytoplasm
Similarity search - Function
Universal stress protein A family / UspA / Universal stress protein family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Universal stress protein MJ0577
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsZarembinski, T.I. / Hung, L.-W. / Mueller-Dieckmann, H.J. / Kim, K.-K. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics.
Authors: Zarembinski, T.I. / Hung, L.-W. / Mueller-Dieckmann, H.J. / Kim, K.-K. / Yokota, H. / Kim, R. / Kim, S.-H.
History
DepositionNov 4, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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.value / _struct_conn.pdbx_dist_value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ATP-BINDING DOMAIN OF PROTEIN MJ0577)
B: PROTEIN (ATP-BINDING DOMAIN OF PROTEIN MJ0577)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8656
Polymers36,7412
Non-polymers1,1244
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-36 kcal/mol
Surface area14880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.530, 96.080, 37.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: Protein PROTEIN (ATP-BINDING DOMAIN OF PROTEIN MJ0577)


Mass: 18370.600 Da / Num. of mol.: 2 / Fragment: ATP-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH ADENOSINE-5'-TRIPHOSPHATE
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Description: RECENTLY SEQUENCED HYPERTHERMOPHILE / Cellular location: CYTOPLASM / Gene: MJ0577 / Plasmid: PET-23A / Production host: Escherichia coli (E. coli) / References: UniProt: Q57997
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 100 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 mg/mlprotein1drop
20.5 mMdithiothreitol1drop
325 mMTris-HCl1drop
48 %PEG40001drop
550 mMimidazole-malate1drop
65 mM1dropMnCl2
716 %PEG40001reservoir
8100 mMimidazole-malate1reservoir
910 mM1reservoirMnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Type: ALS / Wavelength: 0.9683, 0.9799, 0.9806, 1.000
DetectorDetector: CCD / Date: Mar 15, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96831
20.97991
30.98061
411
ReflectionResolution: 1.7→20 Å / Num. obs: 38706 / % possible obs: 98 % / Redundancy: 7.5 % / Rsym value: 0.049
Reflection shellHighest resolution: 1.7 Å / Rsym value: 0.0249 / % possible all: 85.4
Reflection
*PLUS
Num. measured all: 292156 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 85.4 % / Rmerge(I) obs: 0.249

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINEMENT WAS BEGUN WITH CNS AND FINAL REFINEMENT WITH REFMAC AND ARP
RfactorNum. reflection% reflectionSelection details
Rfree0.254 3771 10 %RANDOM
Rwork0.21 ---
obs-37801 97.3 %-
Displacement parametersBiso mean: 30.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2297 0 64 284 2645
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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