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- PDB-3byq: Crystal structure of a duf1185 family protein (bb2672) from borde... -

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Basic information

Entry
Database: PDB / ID: 3byq
TitleCrystal structure of a duf1185 family protein (bb2672) from bordetella bronchiseptica rb50 at 1.70 A resolution
ComponentsUncharacterized protein DUF1185
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyBB2672 / Amino acid synthesis, putative / BB2672 superfamily / Amino acid synthesis / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesBordetella bronchiseptica RB50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism.
Authors: Bakolitsa, C. / Kumar, A. / Jin, K.K. / McMullan, D. / Krishna, S.S. / Miller, M.D. / Abdubek, P. / Acosta, C. / Astakhova, T. / Axelrod, H.L. / Burra, P. / Carlton, D. / Chen, C. / Chiu, H. ...Authors: Bakolitsa, C. / Kumar, A. / Jin, K.K. / McMullan, D. / Krishna, S.S. / Miller, M.D. / Abdubek, P. / Acosta, C. / Astakhova, T. / Axelrod, H.L. / Burra, P. / Carlton, D. / Chen, C. / Chiu, H.J. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Elias, Y. / Ellrott, K. / Ernst, D. / Farr, C.L. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Grzechnik, S.K. / Han, G.W. / Jaroszewski, L. / Johnson, H.A. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Marciano, D. / Morse, A.T. / Murphy, K.D. / Nigoghossian, E. / Nopakun, A. / Okach, L. / Paulsen, J. / Puckett, C. / Reyes, R. / Rife, C.L. / Sefcovic, N. / Tien, H.J. / Trame, C.B. / Trout, C.V. / van den Bedem, H. / Weekes, D. / White, A. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionJan 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: 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 24, 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
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein DUF1185
B: Uncharacterized protein DUF1185
C: Uncharacterized protein DUF1185
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,42536
Polymers64,2193
Non-polymers2,20633
Water10,196566
1
A: Uncharacterized protein DUF1185
B: Uncharacterized protein DUF1185
C: Uncharacterized protein DUF1185
hetero molecules

A: Uncharacterized protein DUF1185
B: Uncharacterized protein DUF1185
C: Uncharacterized protein DUF1185
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,85072
Polymers128,4386
Non-polymers4,41266
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.542, 133.127, 92.544
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-256-

HOH

21C-377-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A HEXAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein DUF1185


Mass: 21406.338 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica RB50 (bacteria)
Species: Bordetella bronchiseptica / Strain: RB50 / NCTC 13252 / Gene: NP_889209.1, BB2672 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q7WJ28, UniProt: A0A0H3LTD0*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: NANODROP, 20% PEG 8000, 0.1M CHES pH 9.5, 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: 0.97912 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 5, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.7→29.854 Å / Num. obs: 65104 / % possible obs: 99.2 % / Redundancy: 5 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.7450.7161.12309946420.71696.6
1.74-1.7950.6111.32249745400.61197.1
1.79-1.8450.4681.62205944510.46897.9
1.84-1.94.90.37622152443490.37698.4
1.9-1.9650.3132.42110242550.31398.9
1.96-2.0350.25132050441140.25199.6
2.03-2.1150.2043.72010040350.20499.9
2.11-2.1950.1754.21939138770.175100
2.19-2.2950.14851863737110.148100
2.29-2.450.1375.31780235440.137100
2.4-2.5350.1255.81715034160.125100
2.53-2.6950.1146.11613332130.114100
2.69-2.8750.1046.61510630170.104100
2.87-3.150.0867.81419028410.086100
3.1-3.450.079.41292525930.07100
3.4-3.850.05911.21177423770.059100
3.8-4.394.90.05212.51042021210.052100
4.39-5.384.80.0513865617890.05100
5.38-7.64.70.05711.7655814100.057100
7.6-29.8544.30.0512.434778090.0598.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→29.854 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.506 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.085
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. CL IONS, EDO, AND PEG 8000 (PG4) FROM THE CRYSTALLIZATION/CRYO SOLUTIONS ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.169 3297 5.1 %RANDOM
Rwork0.138 ---
obs0.139 65081 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.995 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2--1.94 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4361 0 130 566 5057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224666
X-RAY DIFFRACTIONr_bond_other_d0.0030.023245
X-RAY DIFFRACTIONr_angle_refined_deg1.641.9786302
X-RAY DIFFRACTIONr_angle_other_deg1.39637887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4115609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36722.222180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.50915762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.911540
X-RAY DIFFRACTIONr_chiral_restr0.1050.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215137
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02925
X-RAY DIFFRACTIONr_mcbond_it1.66432912
X-RAY DIFFRACTIONr_mcbond_other0.54131183
X-RAY DIFFRACTIONr_mcangle_it2.42954697
X-RAY DIFFRACTIONr_scbond_it3.96781754
X-RAY DIFFRACTIONr_scangle_it5.634111587
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 228 -
Rwork0.207 4413 -
all-4641 -
obs--96.21 %
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)
10.51390.03960.05160.1710.09730.8034-0.02760.0627-0.0229-0.0123-0.0024-0.010.12030.02610.03-0.01740.00250.0034-0.1041-0.0021-0.03433.2837.48814.073
20.39050.0255-0.0140.23920.02630.61560.0241-0.00810.0044-0.01370.0094-0.03480.00460.0682-0.0335-0.0566-0.01190.0082-0.05460.0003-0.031818.47930.44810.472
30.52220.0192-0.03540.25180.08030.72840.0510.00490.1046-0.02850.00890.0123-0.1687-0.0213-0.0598-0.0059-0.00830.0282-0.07590.0088-0.00816.41945.64310.804
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1923 - 193
2X-RAY DIFFRACTION2BB1 - 1922 - 193
3X-RAY DIFFRACTION3CC2 - 1923 - 193

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