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- PDB-3k4w: CRYSTAL STRUCTURE OF Uncharacterized Tim-Barrel Protein Bb4693 Fr... -

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Entry
Database: PDB / ID: 3k4w
TitleCRYSTAL STRUCTURE OF Uncharacterized Tim-Barrel Protein Bb4693 From Bordetella Bronchiseptica
Componentsuncharacterized protein Bb4693
Keywordsstructural genomics / unknown function / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / HYDROLASE / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


secondary metabolic process / carboxy-lyase activity / hydrolase activity / cytoplasm
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Amidohydrolase-related domain-containing protein / Amidohydro-rel domain-containing protein
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsMalashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF Uncharacterized Tim-Barrel Protein Bb4693 From Bordetella Bronchiseptica
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionOct 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 24, 2012Group: Structure summary
Revision 1.3Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.4Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 10, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.6Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein Bb4693
B: uncharacterized protein Bb4693
C: uncharacterized protein Bb4693
D: uncharacterized protein Bb4693
E: uncharacterized protein Bb4693
F: uncharacterized protein Bb4693
G: uncharacterized protein Bb4693
H: uncharacterized protein Bb4693
I: uncharacterized protein Bb4693
J: uncharacterized protein Bb4693
K: uncharacterized protein Bb4693
L: uncharacterized protein Bb4693


Theoretical massNumber of molelcules
Total (without water)392,60912
Polymers392,60912
Non-polymers00
Water34,2831903
1
A: uncharacterized protein Bb4693
B: uncharacterized protein Bb4693
C: uncharacterized protein Bb4693


Theoretical massNumber of molelcules
Total (without water)98,1523
Polymers98,1523
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-21 kcal/mol
Surface area28560 Å2
MethodPISA
2
D: uncharacterized protein Bb4693
E: uncharacterized protein Bb4693
F: uncharacterized protein Bb4693


Theoretical massNumber of molelcules
Total (without water)98,1523
Polymers98,1523
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-20 kcal/mol
Surface area29360 Å2
MethodPISA
3
G: uncharacterized protein Bb4693
H: uncharacterized protein Bb4693
I: uncharacterized protein Bb4693


Theoretical massNumber of molelcules
Total (without water)98,1523
Polymers98,1523
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-21 kcal/mol
Surface area29200 Å2
MethodPISA
4
J: uncharacterized protein Bb4693
K: uncharacterized protein Bb4693
L: uncharacterized protein Bb4693


Theoretical massNumber of molelcules
Total (without water)98,1523
Polymers98,1523
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-21 kcal/mol
Surface area30010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.923, 248.768, 90.618
Angle α, β, γ (deg.)90.00, 104.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
uncharacterized protein Bb4693


Mass: 32717.412 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: RB50 / Gene: BB4693 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q7WEE2, UniProt: A0A0H3M034*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1903 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 298 K / pH: 5.6
Details: 30% PEG 4000, 0.1 M Na-citrate, 0.2 M ammonium acetate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9791
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.92→25.977 Å / Num. obs: 270144 / % possible obs: 98.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.201 / Rsym value: 0.201 / Net I/σ(I): 5.2
Reflection shellResolution: 1.92→2.02 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.02 / Mean I/σ(I) obs: 0.3 / Rsym value: 2.044 / % possible all: 94.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.2 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å25.98 Å
Translation2.5 Å25.98 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.5data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→25.97 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.5 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 13295 5.1 %RANDOM
Rwork0.191 ---
obs0.194 262839 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.92→25.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26544 0 0 1903 28447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02227434
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.96437367
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59153428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77123.4291286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.547154415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.70915218
X-RAY DIFFRACTIONr_chiral_restr0.1350.24030
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02121400
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0641.516986
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.834227444
X-RAY DIFFRACTIONr_scbond_it3.292310448
X-RAY DIFFRACTIONr_scangle_it5.0484.59889
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 784 -
Rwork0.341 14112 -
obs--73.58 %
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)
10.85040.029-0.18380.48970.01830.2223-0.0240.0799-0.0388-0.07920.0098-0.01570.0149-0.04430.01420.0175-0.0052-0.00220.020.01090.04645.5673-64.216232.336
21.12270.0476-0.03290.30020.07130.48570.0399-0.1184-0.06120.0848-0.0478-0.0170.0049-0.01580.0080.0314-0.02-0.01140.02220.00750.0332.7577-35.845557.0957
30.6082-0.01780.10780.5403-0.08080.188-0.00210.08480.0184-0.0279-0.0169-0.071-0.02250.00430.0190.01770.00850.01630.01840.0130.02786.1075-28.613319.8692
41.3753-0.37640.21480.4585-0.15880.3908-0.0613-0.1998-0.04810.08420.0654-0.0102-0.025-0.0352-0.00410.01870.00890.00280.03080.00450.0263-36.7228-57.971150.0326
50.6970.2405-0.10140.39880.02030.3495-0.0520.1227-0.0128-0.0750.0185-0.00360.0206-0.0050.03350.0340.0096-0.00030.0392-0.00530.0048-34.1665-50.975112.6583
60.5768-0.00390.1040.6444-0.03010.29330.0188-0.03460.0412-0.0218-0.01360.0415-0.04520.0135-0.00520.0189-0.00150.00730.0066-0.01110.0439-37.2697-22.307237.977
70.52150.09820.3310.31640.00380.95970.03810.0211-0.09360.00580.02860.0220.0861-0.0863-0.06660.0925-0.0057-0.02090.0242-0.01340.042-63.8028-4.137172.9971
80.5948-0.09630.15980.38620.10980.75120.06680.1132-0.02120.0011-0.0271-0.0330.05620.1642-0.03960.05510.02720.00390.1068-0.01440.0078-31.34914.272566.5691
90.5697-0.1414-0.14110.3775-0.03350.2880.02170.09360.0873-0.01030.0093-0.0170.0136-0.0566-0.0310.0420.00980.00430.04860.01710.0139-64.988532.241963.967
100.5055-0.19630.01570.40660.12530.38170.00430.00620.0048-0.02790.0361-0.0357-0.00960.0562-0.04050.0487-0.00040.0110.0097-0.00680.0072-16.55995.33123.8733
110.62050.0996-0.03920.3549-0.12570.67950.0306-0.03360.03720.02380.00980.0395-0.0273-0.0671-0.04040.05850.01950.01590.02480.00070.0117-50.139323.142621.0458
120.38-0.12240.05940.47660.21920.4265-0.0050.01890.08510.01710.033-0.0409-0.0670.0337-0.0280.0809-0.01970.01680.0184-0.01260.0415-17.565342.26315.0959
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 281
2X-RAY DIFFRACTION1A290 - 2087
3X-RAY DIFFRACTION2B1 - 281
4X-RAY DIFFRACTION2B290 - 2072
5X-RAY DIFFRACTION3C1 - 281
6X-RAY DIFFRACTION3C290 - 2063
7X-RAY DIFFRACTION4D1 - 281
8X-RAY DIFFRACTION4D290 - 2066
9X-RAY DIFFRACTION5E1 - 281
10X-RAY DIFFRACTION5E290 - 2086
11X-RAY DIFFRACTION6F1 - 281
12X-RAY DIFFRACTION6F290 - 2084
13X-RAY DIFFRACTION7G1 - 281
14X-RAY DIFFRACTION7G290 - 2048
15X-RAY DIFFRACTION8H1 - 281
16X-RAY DIFFRACTION8H290 - 2079
17X-RAY DIFFRACTION9I1 - 281
18X-RAY DIFFRACTION9I290 - 2026
19X-RAY DIFFRACTION10J1 - 281
20X-RAY DIFFRACTION10J290 - 2083
21X-RAY DIFFRACTION11K1 - 281
22X-RAY DIFFRACTION11K290 - 2081
23X-RAY DIFFRACTION12L1 - 281
24X-RAY DIFFRACTION12L290 - 2078

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