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- PDB-3ira: The crystal structure of one domain of the conserved protein from... -

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Basic information

Entry
Database: PDB / ID: 3ira
TitleThe crystal structure of one domain of the conserved protein from Methanosarcina mazei Go1
ComponentsConserved protein
Keywordsstructural genomics / unknown function / conserved protein / Methanosarcina mazei / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


Domain of unknown function DUF255 / Spermatogenesis-associated protein 20 / Protein of unknown function, DUF255 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsZhang, R. / Wu, R. / Keigher, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of one domain of the conserved protein from Methanosarcina mazei Go1
Authors: Zhang, R. / Wu, R. / Keigher, L. / Joachimiak, A.
History
DepositionAug 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved protein


Theoretical massNumber of molelcules
Total (without water)20,1161
Polymers20,1161
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.843, 63.843, 95.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Conserved protein


Mass: 20115.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: Go1 / Gene: GI:20905010, MM_0619 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8PZ75
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M ammonium acetate, 0.1M HEPES, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.9796
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2009 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
ReflectionResolution: 2.1→53.15 Å / Num. all: 11549 / Num. obs: 11532 / % possible obs: 99.85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 17.8 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 35.92
Reflection shellResolution: 2.1→2.154 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.93 / Num. unique all: 867 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→53.15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.952 / SU B: 9.83 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 1.93 / ESU R: 0.205 / ESU R Free: 0.167
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21783 580 4.8 %RANDOM
Rwork0.18696 ---
obs0.18849 11532 99.85 %-
all-11594 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.189 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2--1.09 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.1→53.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 0 73 1481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221447
X-RAY DIFFRACTIONr_bond_other_d0.0010.021007
X-RAY DIFFRACTIONr_angle_refined_deg1.81.9491959
X-RAY DIFFRACTIONr_angle_other_deg1.0063.0022455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7575171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74524.78971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16115260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.725157
X-RAY DIFFRACTIONr_chiral_restr0.1270.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211584
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02282
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9061.5861
X-RAY DIFFRACTIONr_mcbond_other0.241.5340
X-RAY DIFFRACTIONr_mcangle_it1.80621401
X-RAY DIFFRACTIONr_scbond_it3.0933586
X-RAY DIFFRACTIONr_scangle_it5.1514.5558
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 39 -
Rwork0.201 828 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 20.265 Å / Origin y: 12.139 Å / Origin z: 27.166 Å
111213212223313233
T0.0862 Å2-0.0119 Å2-0.0202 Å2-0.0336 Å20.0002 Å2--0.0103 Å2
L0.8604 °2-0.3683 °2-0.2571 °2-1.3088 °20.6897 °2--2.8819 °2
S-0.0221 Å °-0.0201 Å °0.0063 Å °-0.153 Å °-0.0307 Å °0.0705 Å °-0.2354 Å °-0.022 Å °0.0528 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 30
2X-RAY DIFFRACTION1A31 - 60
3X-RAY DIFFRACTION1A61 - 90
4X-RAY DIFFRACTION1A91 - 120
5X-RAY DIFFRACTION1A121 - 150
6X-RAY DIFFRACTION1A151 - 171

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