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- PDB-2go8: Crystal structure of YQJZ_BACSU FROM Bacillus subtilis. Northeast... -

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Basic information

Entry
Database: PDB / ID: 2go8
TitleCrystal structure of YQJZ_BACSU FROM Bacillus subtilis. Northeast structural genomics TARGET SR435
ComponentsHypothetical protein yqjZ
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SR435 / protein structure / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyABM 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 / Uncharacterized protein YqjZ
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsBenach, J. / Su, M. / Jayaraman, S. / Fang, Y. / Xiao, R. / Ma, L.-C. / Cunningham, K. / Wang, D. / Acton, T.B. / Montelione, G.T. ...Benach, J. / Su, M. / Jayaraman, S. / Fang, Y. / Xiao, R. / Ma, L.-C. / Cunningham, K. / Wang, D. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of YQJZ_BACSU from Bacillus subtilis. Northeast Structural Genomics TARGET SR435
Authors: Benach, J. / Su, M. / Jayaraman, S. / Fang, Y. / Xiao, R. / Ma, L.-C. / Cunningham, K. / Wang, D. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionApr 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein yqjZ


Theoretical massNumber of molelcules
Total (without water)14,3241
Polymers14,3241
Non-polymers00
Water2,450136
1
A: Hypothetical protein yqjZ

A: Hypothetical protein yqjZ


Theoretical massNumber of molelcules
Total (without water)28,6482
Polymers28,6482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3530 Å2
ΔGint-7 kcal/mol
Surface area10120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.076, 59.650, 73.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological assembly is generated by: -x, y, -z+1/2 and the translation (1 0 0)

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Components

#1: Protein Hypothetical protein yqjZ


Mass: 14324.112 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yqjZ / Plasmid: pet21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: P54563
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.19 Å3/Da / Density % sol: 39.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG400, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791, 0.9794, 0.9678
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
30.96781
Reflection

D res high: 2.1 Å / D res low: 20 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
8.1118.51067590.1051.041310096.9
8.22191046180.1031.021280396.9
8.1317.41062840.1091.061320097
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.152091199.710.0661.0288.4
4.15.1589699.810.0750.9648.7
3.594.186394.510.0860.9576.2
3.263.5989210010.0930.8958.7
3.033.2691610010.11.0729
2.853.0387410010.110.9778.9
2.712.8590310010.1371.18.9
2.592.7192110010.1660.8868.8
2.492.5988810010.1871.0578.9
2.42.4989910010.2071.0938.9
2.332.490910010.2471.0688.8
2.262.337298110.3081.1785.6
2.22.267327910.2991.2874.7
2.152.286410010.3121.138.4
2.12.1590310010.3531.1458.1
5.152088899.720.0661.0378.5
4.15.1588199.920.0730.9478.7
3.594.183794.920.0850.9416.6
3.263.5988999.420.0920.8588.3
3.033.2687110020.0981.0578.9
2.853.0386710020.1060.9058.9
2.712.8589410020.1321.0678.9
2.592.7187410020.1590.868.8
2.492.5989110020.1751.0079
2.42.4989810020.21.0828.9
2.332.486510020.231.0688.8
2.262.3377288.420.3231.1127.2
2.22.2661570.320.2841.1752.9
2.152.289499.920.3341.1938.1
2.12.1586710020.3181.1398.4
5.152092099.830.071.1718.3
4.15.1590110030.0750.9938.7
3.594.186894.330.0890.9986.2
3.263.5990210030.0930.8728.7
3.033.2689910030.1021.0898.8
2.853.0390910030.1110.9738.8
2.712.8589610030.1431.1348.8
2.592.7192710030.1730.9168.7
2.492.5990610030.1951.0558.7
2.42.4989010030.2151.1028.6
2.332.490810030.2631.0558.6
2.262.3373981.230.3371.2415.3
2.22.2674279.630.3511.2215.2
2.152.286210030.3391.148.3
2.12.1593110030.3961.1937.9
ReflectionResolution: 2.1→20 Å / Num. all: 13100 / Num. obs: 13100 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.105 / Χ2: 1.042 / Net I/σ(I): 18.5
Reflection shellResolution: 2.1→2.15 Å / % possible obs: 100 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.353 / Num. unique obs: 903 / Χ2: 1.145 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97915.09-8.01
13 wavelength20.97941.92-7.2
13 wavelength30.96783.29-4.94
Phasing dmFOM : 0.7 / FOM acentric: 0.68 / FOM centric: 0.79 / Reflection: 3754 / Reflection acentric: 3137 / Reflection centric: 617
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.4-19.9271.391.091.8917811167
4.6-7.40.880.90.82530406124
3.7-4.60.850.860.84630518112
3.3-3.70.780.770.8662153289
2.8-3.30.580.590.481116972144
2.6-2.80.370.390.2567959881

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
RESOLVE2.08phasing
CNSrefinement
PDB_EXTRACT1.701data extraction
ADSCdata collection
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / FOM work R set: 0.834 / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 874 8.7 %random
Rwork0.23 ---
all-8962 --
obs-8962 89.6 %-
Solvent computationBsol: 64.176 Å2
Displacement parametersBiso mean: 42.641 Å2
Baniso -1Baniso -2Baniso -3
1--23.484 Å20 Å20 Å2
2--12.426 Å20 Å2
3---11.058 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms717 0 0 136 853
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.3-2.350.305510.272445496
2.35-2.40.251310.234430461
2.4-2.450.225590.215465524
2.45-2.510.245470.216484531
2.51-2.580.287500.229479529
2.58-2.660.299580.274493551
2.66-2.740.28500.247500550
2.74-2.840.278470.252520567
2.84-2.960.284520.237498550
2.96-3.090.367620.25519581
3.09-3.250.232770.189483560
3.25-3.450.208470.219524571
3.45-3.720.245350.224320355
3.72-4.090.315500.201403453
4.09-4.680.169490.183530579
4.68-5.870.251590.229516575
5.87-200.273500.313479529
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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