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- PDB-3ke2: CRYSTAL STRUCTURE OF a DUF2131 family protein (SAMA_2911) FROM SH... -

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Basic information

Entry
Database: PDB / ID: 3ke2
TitleCRYSTAL STRUCTURE OF a DUF2131 family protein (SAMA_2911) FROM SHEWANELLA AMAZONENSIS SB2B AT 2.50 A RESOLUTION
Componentsuncharacterized protein YP_928783.1
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyUncharacterised conserved protein UCP037266 / Winged helix-turn helix / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / NITRATE ION / Helix-turn-helix domain-containing protein
Function and homology information
Biological speciesShewanella amazonensis SB2B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of STRUCTURAL GENOMICS, UNKNOWN FUNCTION (YP_928783.1) from SHEWANELLA AMAZONENSIS SB2B at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: uncharacterized protein YP_928783.1
B: uncharacterized protein YP_928783.1
C: uncharacterized protein YP_928783.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3168
Polymers39,0063
Non-polymers3105
Water1,08160
1
A: uncharacterized protein YP_928783.1
B: uncharacterized protein YP_928783.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1284
Polymers26,0042
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-6 kcal/mol
Surface area11440 Å2
MethodPISA
2
C: uncharacterized protein YP_928783.1
hetero molecules

C: uncharacterized protein YP_928783.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3768
Polymers26,0042
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1970 Å2
ΔGint2 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.479, 100.509, 114.583
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-127-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A10 - 67
2114B10 - 67
3114C10 - 67
1216A68 - 74
2216B68 - 74
3216C68 - 74
1314A75 - 103
2314B75 - 103
3314C75 - 103
DetailsCRYSTAL PACKING ANALYSIS AND STATIC LIGHT SCATTERING WITH ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein uncharacterized protein YP_928783.1


Mass: 13001.906 Da / Num. of mol.: 3 / Mutation: D107V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella amazonensis SB2B (bacteria) / Strain: ATCC BAA-1098 / SB2B / Gene: Sama_2911 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1S9Q7
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DNA SEQUENCING OF THE CLONED CONSTRUCT SHOWS A VALINE AT POSITION 107 INSTEAD OF AN ASPARTATE. THE VALINE AT POSITION 107 IS SUPPORTED BY THE ELECTRON DENSITY

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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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.2000M K2NO3, 20.0000% PEG-3350, No Buffer pH 6.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162,0.97917
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 8, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979171
ReflectionResolution: 2.5→29.921 Å / Num. obs: 13572 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 51.638 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.08
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.5-2.590.4231.848912530198.3
2.59-2.690.3242.447412444199.1
2.69-2.810.2523.249052521198.8
2.81-2.960.1744.550042574199.3
2.96-3.150.126.451572642199
3.15-3.390.0769.748432499199
3.39-3.730.04715.149262527198.8
3.73-4.260.03321.248952509198.7
4.26-5.350.02725.749822545198.6
5.35-29.9210.02230.550702561197.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.921 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 0.19 / SU B: 23.302 / SU ML: 0.227 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.484 / ESU R Free: 0.281
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. TLS GROUPS WERE ASSIGNED WITH THE AID OF TLS MOTION SERVER. 5. NITRATE IONS (NO3)FROM THE CRYSTALLIZATION SOLUTION; AND ETHYLENE GLYCOLS (EDO)USED AS A CRYOPROTECTANT ARE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 667 4.9 %RANDOM
Rwork0.214 ---
obs0.216 13554 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.15 Å2 / Biso mean: 22.077 Å2 / Biso min: 6.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2---1.24 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2318 0 20 60 2398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212439
X-RAY DIFFRACTIONr_bond_other_d0.0010.021664
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9433296
X-RAY DIFFRACTIONr_angle_other_deg0.85134019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3055309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.17322.564117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.60315419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7631524
X-RAY DIFFRACTIONr_chiral_restr0.0520.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022746
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02532
X-RAY DIFFRACTIONr_mcbond_it0.4621.51493
X-RAY DIFFRACTIONr_mcbond_other0.0971.5614
X-RAY DIFFRACTIONr_mcangle_it0.90122368
X-RAY DIFFRACTIONr_scbond_it1.5463946
X-RAY DIFFRACTIONr_scangle_it2.4124.5920
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1076MEDIUM POSITIONAL0.330.5
2B1076MEDIUM POSITIONAL0.390.5
3C1076MEDIUM POSITIONAL0.430.5
1A93LOOSE POSITIONAL0.775
2B93LOOSE POSITIONAL1.215
3C93LOOSE POSITIONAL1.55
1A1076MEDIUM THERMAL0.492
2B1076MEDIUM THERMAL0.452
3C1076MEDIUM THERMAL0.532
1A93LOOSE THERMAL0.9310
2B93LOOSE THERMAL0.9610
3C93LOOSE THERMAL1.0710
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.478 53 -
Rwork0.33 914 -
all-967 -
obs--99.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0737-1.6778-0.64354.83381.55482.75280.09980.0267-0.1752-0.2906-0.00220.03430.0463-0.0406-0.09760.14840.018-0.03220.01090.01530.218920.99241.28643.428
21.6875-2.2089-0.74424.72180.61692.3992-0.2637-0.4150.06060.56090.3440.02680.0216-0.0817-0.08030.16250.0887-0.05680.192-0.00910.287736.38418.88648.71
36.6280.4843-0.49321.3831-0.11262.20250.007-0.64650.01310.1393-0.0050.02830.0511-0.0971-0.00190.0585-0.0288-0.02640.1061-0.01440.185412.66911.65133.348
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 110
2X-RAY DIFFRACTION2B11 - 106
3X-RAY DIFFRACTION3C11 - 107

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