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- PDB-1xuv: X-Ray Crystal Structure of Protein MM0500 from Methanosarcina maz... -

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Basic information

Entry
Database: PDB / ID: 1xuv
TitleX-Ray Crystal Structure of Protein MM0500 from Methanosarcina mazei. Northeast Structural Genomics Consortium Target MaR10.
Componentshypothetical protein MM0500
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Alpha-beta protein / Northeast Structural Genomics Consortium / NESG / Protein Structure Initiative / PSI
Function / homologyActivator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Activator of Hsp90 ATPase homologue 1/2-like C-terminal domain-containing protein
Function and homology information
Biological speciesMethanosarcina mazei Go1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsForouhar, F. / Abashidze, M. / Ciano, M. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Hypothetical Protein from Methanosarcina mazei, Northeast Strcutural Genomics Target MaR10
Authors: Forouhar, F. / Abashidze, M. / Ciano, M. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / struct_biol / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein MM0500
B: hypothetical protein MM0500
C: hypothetical protein MM0500


Theoretical massNumber of molelcules
Total (without water)62,0873
Polymers62,0873
Non-polymers00
Water4,450247
1
A: hypothetical protein MM0500
C: hypothetical protein MM0500


Theoretical massNumber of molelcules
Total (without water)41,3912
Polymers41,3912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein MM0500

B: hypothetical protein MM0500


Theoretical massNumber of molelcules
Total (without water)41,3912
Polymers41,3912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Unit cell
Length a, b, c (Å)103.829, 59.941, 95.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MC121
Detailspossibly dimer

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Components

#1: Protein hypothetical protein MM0500 / Aha1 Domain / MAR10


Mass: 20695.639 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Species: Methanosarcina mazei / Strain: Goe1 / Plasmid: BL21(DE3)+Magic / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PZJ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM Acetate (pH 4.6), 8% PEG 4k, 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 14, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 67882 / Num. obs: 66458 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.035 / Net I/σ(I): 29.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.6 / Num. unique all: 6697 / Rsym value: 0.211 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→28.59 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 489385.78 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 5901 9.8 %RANDOM
Rwork0.231 ---
all0.234 66458 --
obs0.231 60190 89.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.9852 Å2 / ksol: 0.338881 e/Å3
Displacement parametersBiso mean: 43.1 Å2
Baniso -1Baniso -2Baniso -3
1--6.25 Å20 Å20 Å2
2---5.54 Å20 Å2
3---11.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.1→28.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3966 0 0 247 4213
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 835 10.3 %
Rwork0.265 7237 -
obs-6697 72.1 %

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