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- PDB-4dpo: Crystal structure of a conserved protein MM_1583 from Methanosarc... -

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Basic information

Entry
Database: PDB / ID: 4dpo
TitleCrystal structure of a conserved protein MM_1583 from Methanosarcina mazei Go1
ComponentsConserved protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Putative antibitic biosynthesis mono oxygenase
Function / homology
Function and homology information


: / ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.73 Å
AuthorsAgarwal, R. / Chamala, S. / Evans, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Foti, R. / Siedel, R. / Zencheck, W. ...Agarwal, R. / Chamala, S. / Evans, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Foti, R. / Siedel, R. / Zencheck, W. / Villigas, G. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a conserved protein MM_1583 from Methanosarcina mazei Go1
Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S.
History
DepositionFeb 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Nov 27, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved protein
B: Conserved protein


Theoretical massNumber of molelcules
Total (without water)28,4992
Polymers28,4992
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-5 kcal/mol
Surface area10510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.761, 60.255, 104.312
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Conserved protein


Mass: 14249.553 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: Go1 / Gene: MM_1583 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q8PWK2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.29 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, pH 8.5, 2M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2012 / Details: Mirrors
RadiationMonochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.71→50 Å / Num. all: 10299 / Num. obs: 10299 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8
Reflection shellResolution: 2.71→2.81 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 5 / Num. unique all: 1024 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
AutoSolphasing
Cootmodel building
CCP4model building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: SAD
Starting model: None

Resolution: 2.73→39.43 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.907 / SU B: 11.305 / SU ML: 0.231 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.436 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28291 490 4.8 %RANDOM
Rwork0.23607 ---
obs0.23826 9723 97.05 %-
all-10299 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.73→39.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1549 0 0 5 1554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221566
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.9612129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1775201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5192670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.72915250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.554153
X-RAY DIFFRACTIONr_chiral_restr0.120.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211183
X-RAY DIFFRACTIONr_mcbond_it0.9541.51012
X-RAY DIFFRACTIONr_mcangle_it1.85821608
X-RAY DIFFRACTIONr_scbond_it3.0673554
X-RAY DIFFRACTIONr_scangle_it4.8064.5521
LS refinement shellResolution: 2.726→2.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.497 26 -
Rwork0.331 592 -
obs--82.29 %

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