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- PDB-2av9: Crystal Structure of the PA5185 protein from Pseudomonas Aerugino... -

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Basic information

Entry
Database: PDB / ID: 2av9
TitleCrystal Structure of the PA5185 protein from Pseudomonas Aeruginosa Strain PAO1.
ComponentsThioesterase
KeywordsHYDROLASE / thioesterase / structural genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyThioesterase-like superfamily / fatty acyl-CoA hydrolase activity / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsChruszcz, M. / Wang, S. / Cymborowski, M. / Kudritska, M. / Evdokimova, E. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Cryst.Growth Des. / Year: 2008
Title: Function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase PA5185 from Pseudomonas aeruginosa PAO1.
Authors: Chruszcz, M. / Zimmerman, M.D. / Wang, S. / Koclega, K.D. / Zheng, H. / Evdokimova, E. / Kudritska, M. / Cymborowski, M. / Savchenko, A. / Edwards, A. / Minor, W.
History
DepositionAug 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Thioesterase
B: Thioesterase
C: Thioesterase
D: Thioesterase
E: Thioesterase
F: Thioesterase
G: Thioesterase
H: Thioesterase
I: Thioesterase
J: Thioesterase
K: Thioesterase
L: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,77127
Polymers198,33012
Non-polymers1,44115
Water1,06359
1
A: Thioesterase
B: Thioesterase
D: Thioesterase
E: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5909
Polymers66,1104
Non-polymers4805
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-114 kcal/mol
Surface area21760 Å2
MethodPISA
2
C: Thioesterase
H: Thioesterase
I: Thioesterase
K: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4948
Polymers66,1104
Non-polymers3844
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8890 Å2
ΔGint-87 kcal/mol
Surface area21470 Å2
MethodPISA
3
F: Thioesterase
G: Thioesterase
J: Thioesterase
L: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,68610
Polymers66,1104
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-126 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)241.661, 64.384, 117.469
Angle α, β, γ (deg.)90.00, 105.40, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21G
31H
41I
51L
61A
71G
81H
91I
101L
111A
121G
131H
141I
151L
12A
22E
32F
42B
52C
62D
72J
82K
92A
102E
112F
122B
132C
142D
152J
162K
172A
182E
192F
202B
212C
222D
232J
242K
252A
262E
272F
282B
292C
302D
312J
322K
13E
23F
33B
14A
24I
34J
44K
54L
64C
74D
84G
94H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEUGLU2AA8 - 508 - 50
211LEUGLU2GG8 - 508 - 50
311LEUGLU2HH8 - 508 - 50
411LEUGLU2II8 - 508 - 50
511LEUGLU2LL8 - 508 - 50
621GLUGLU2AA60 - 12260 - 122
721GLUGLU2GG60 - 12260 - 122
821GLUGLU2HH60 - 12260 - 122
921GLUGLU2II60 - 12260 - 122
1021GLUGLU2LL60 - 12260 - 122
1131ARGGLN2AA127 - 143127 - 143
1231ARGGLN2GG127 - 143127 - 143
1331ARGGLN2HH127 - 143127 - 143
1431ARGGLN2II127 - 143127 - 143
1531ARGGLN2LL127 - 143127 - 143
112LEUGLU2AA8 - 508 - 50
212LEUGLU2EE8 - 508 - 50
312LEUGLU2FF8 - 508 - 50
412LEUGLU2BB8 - 508 - 50
512LEUGLU2CC8 - 508 - 50
612LEUGLU2DD8 - 508 - 50
712LEUGLU2JJ8 - 508 - 50
812LEUGLU2KK8 - 508 - 50
922GLULEU2AA60 - 10460 - 104
1022GLULEU2EE60 - 10460 - 104
1122GLULEU2FF60 - 10460 - 104
1222GLULEU2BB60 - 10460 - 104
1322GLULEU2CC60 - 10460 - 104
1422GLULEU2DD60 - 10460 - 104
1522GLULEU2JJ60 - 10460 - 104
1622GLULEU2KK60 - 10460 - 104
1732GLUGLU2AA109 - 122109 - 122
1832GLUGLU2EE109 - 122109 - 122
1932GLUGLU2FF109 - 122109 - 122
2032GLUGLU2BB109 - 122109 - 122
2132GLUGLU2CC109 - 122109 - 122
2232GLUGLU2DD109 - 122109 - 122
2332GLUGLU2JJ109 - 122109 - 122
2432GLUGLU2KK109 - 122109 - 122
2542ARGGLN2AA127 - 143127 - 143
2642ARGGLN2EE127 - 143127 - 143
2742ARGGLN2FF127 - 143127 - 143
2842ARGGLN2BB127 - 143127 - 143
2942ARGGLN2CC127 - 143127 - 143
3042ARGGLN2DD127 - 143127 - 143
3142ARGGLN2JJ127 - 143127 - 143
3242ARGGLN2KK127 - 143127 - 143
113GLUGLU1EE50 - 6050 - 60
213GLUGLU1FF50 - 6050 - 60
313GLUGLU1BB50 - 6050 - 60
114GLUGLU1AA50 - 6050 - 60
214GLUGLU1II50 - 6050 - 60
314GLUGLU1JJ50 - 6050 - 60
414GLUGLU1KK50 - 6050 - 60
514GLUGLU1LL50 - 6050 - 60
614GLUGLU1CC50 - 6050 - 60
714GLUGLU1DD50 - 6050 - 60
814GLUGLU1GG50 - 6050 - 60
914GLUGLU1HH50 - 6050 - 60

NCS ensembles :
ID
1
2
3
4
DetailsThe most probable biological assembly is a tetramer. Chains C,H, I and K create the tetramer.

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Components

#1: Protein
Thioesterase


Mass: 16527.473 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q9HU04
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Ammonium Sulphate, 0.1M Bis-Tris pH 5.5, 23% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97943, 0.97929, 0.96420
DetectorType: SBC-3 / Detector: CCD / Date: May 5, 2004 / Details: mirror
RadiationMonochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979431
20.979291
30.96421
ReflectionResolution: 2.4→36.94 Å / Num. all: 68671 / Num. obs: 68671 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.2 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
SHARPphasing
ARP/wARPmodel building
CCP4phasing
SHELXEmodel building
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.4→36.94 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.91 / SU B: 18.763 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.466 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25334 3473 5.1 %RANDOM
Rwork0.20402 ---
obs0.20653 65081 99.96 %-
all-65081 --
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: 42.481 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20.2 Å2
2---0.1 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.4→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12500 0 75 59 12634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02212897
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9041.93917611
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.62251658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86923.108576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.686151726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3271578
X-RAY DIFFRACTIONr_chiral_restr0.1330.21956
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210080
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.25453
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.28949
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2449
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.2181
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9921.58411
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.685213138
X-RAY DIFFRACTIONr_scbond_it3.40835057
X-RAY DIFFRACTIONr_scangle_it4.8354.54472
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A491tight positional0.10.05
12G491tight positional0.080.05
13H491tight positional0.090.05
14I491tight positional0.090.05
15L491tight positional0.080.05
21A471tight positional0.150.05
22E471tight positional0.140.05
23F471tight positional0.130.05
24B471tight positional0.190.05
25C471tight positional0.130.05
26D471tight positional0.140.05
27J471tight positional0.170.05
28K471tight positional0.110.05
31E59tight positional0.080.05
32F59tight positional0.090.05
33B59tight positional0.130.05
41A54tight positional0.070.05
42I54tight positional0.070.05
43J54tight positional0.080.05
44K54tight positional0.080.05
45L54tight positional0.080.05
46C54tight positional0.080.05
47D54tight positional0.070.05
48G54tight positional0.070.05
49H54tight positional0.060.05
11A387medium positional0.40.5
12G387medium positional0.390.5
13H387medium positional0.390.5
14I387medium positional0.370.5
15L387medium positional0.310.5
21A375medium positional0.560.5
22E375medium positional0.610.5
23F375medium positional0.590.5
24B375medium positional0.660.5
25C375medium positional0.560.5
26D375medium positional0.590.5
27J375medium positional0.670.5
28K375medium positional0.610.5
11A491tight thermal0.370.5
12G491tight thermal0.220.5
13H491tight thermal0.260.5
14I491tight thermal0.240.5
15L491tight thermal0.230.5
21A471tight thermal0.40.5
22E471tight thermal0.360.5
23F471tight thermal0.290.5
24B471tight thermal0.380.5
25C471tight thermal0.30.5
26D471tight thermal0.320.5
27J471tight thermal0.340.5
28K471tight thermal0.260.5
31E59tight thermal0.290.5
32F59tight thermal0.220.5
33B59tight thermal0.380.5
41A54tight thermal0.540.5
42I54tight thermal0.260.5
43J54tight thermal0.360.5
44K54tight thermal0.20.5
45L54tight thermal0.170.5
46C54tight thermal0.260.5
47D54tight thermal0.290.5
48G54tight thermal0.130.5
49H54tight thermal0.130.5
11A387medium thermal1.82
12G387medium thermal1.362
13H387medium thermal1.462
14I387medium thermal1.472
15L387medium thermal1.432
21A375medium thermal2.162
22E375medium thermal2.012
23F375medium thermal1.752
24B375medium thermal2.282
25C375medium thermal1.792
26D375medium thermal2.22
27J375medium thermal2.072
28K375medium thermal1.532
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 266 -
Rwork0.237 4741 -
obs--99.76 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.8895-0.0725-0.10052.49190.35641.11030.00510.1959-0.1713-0.13730.0207-0.1239-0.08420.073-0.0258-0.12480.01450.0115-0.27280.0076-0.35444.67446.1567.755
21.66580.4146-0.81911.3781-0.65222.15360.0013-0.2878-0.40580.0483-0.1878-0.285-0.03310.38430.1866-0.1311-0.0524-0.0216-0.18550.0452-0.234867.16310.9645.338
32.44281.580.44081.51830.22042.24160.07290.2245-0.4332-0.12490.2246-0.26830.12320.0133-0.2974-0.10670.029-0.054-0.19350.04940.170969.33737.34767.769
42.4241-0.34230.20872.63350.09792.3746-0.1138-0.5271-0.91120.17150.14280.04640.43350.173-0.029-0.03780.10450.0314-0.15750.23140.000444.32727.77287.269
53.5077-0.306-0.79541.46820.44422.5125-0.2772-0.82-0.53250.28990.15420.29340.11670.15310.123-0.07530.09610.0708-0.05040.2332-0.190226.65538.78994.646
63.85-0.4066-0.56561.3841-0.09742.8688-0.20530.1869-0.81410.0015-0.26210.35910.2113-0.33890.4675-0.1466-0.04260.0612-0.0837-0.0885-0.0071121.0859.02786.858
74.09460.3994-2.11.8147-0.18913.7054-0.14-0.1105-0.5340.2329-0.22790.4581-0.0064-0.91060.3679-0.1138-0.00020.04550.3543-0.15480.0027103.11317.55696.552
83.79830.43211.14941.3373-0.19243.24310.1228-0.6468-0.2850.30610.1206-0.13640.25930.1097-0.24340.05130.1059-0.09320.0826-0.00610.028988.04546.95992.68
93.0172.22460.89715.22831.58912.23620.0067-0.51570.30210.0620.02940.2858-0.151-0.1609-0.0362-0.1040.0848-0.0484-0.0708-0.03240.091169.66857.16885.852
102.49330.2711-1.15281.77690.70792.55010.1208-0.57380.12130.2147-0.1326-0.0271-0.14130.0640.0118-0.0367-0.0209-0.0214-0.0403-0.0514-0.2692132.15131.59897.334
114.01650.91970.49540.7425-0.61413.08450.18980.6174-0.7840.0160.20390.03860.10270.8616-0.3937-0.03730.1184-0.06940.1548-0.2230.145490.95141.17966.935
121.7868-0.2961-0.70251.56841.31393.44820.1465-0.06760.4086-0.0436-0.053-0.2647-0.61190.631-0.09350.1192-0.2067-0.02860.11460.1063-0.084896.80740.4223.251
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1465 - 146
2X-RAY DIFFRACTION2BB6 - 1446 - 144
3X-RAY DIFFRACTION3CC6 - 1446 - 144
4X-RAY DIFFRACTION4DD3 - 1433 - 143
5X-RAY DIFFRACTION5EE7 - 1437 - 143
6X-RAY DIFFRACTION6FF6 - 1446 - 144
7X-RAY DIFFRACTION7GG8 - 1438 - 143
8X-RAY DIFFRACTION8HH5 - 1435 - 143
9X-RAY DIFFRACTION9II6 - 1446 - 144
10X-RAY DIFFRACTION10JJ6 - 1436 - 143
11X-RAY DIFFRACTION11KK7 - 1437 - 143
12X-RAY DIFFRACTION12LL7 - 1437 - 143

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