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- PDB-4go3: Crystal structure of PnpE from Pseudomonas sp. WBC-3 -

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Basic information

Entry
Database: PDB / ID: 4go3
TitleCrystal structure of PnpE from Pseudomonas sp. WBC-3
ComponentsPutative gamma-hydroxymuconic semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / gamma-hydroxymuconic semialdehyde dehydrogenase
Function / homology
Function and homology information


: / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal ...Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative gamma-hydroxymuconic semialdehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas (RNA similarity group I)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 Å
AuthorsSu, J. / Zhang, C. / Liu, S. / Zhu, D. / Gu, L.
CitationJournal: To be Published
Title: Crystal structure of PnpE from Pseudomonas sp. WBC-3
Authors: Su, J. / Zhang, C. / Liu, S. / Zhu, D. / Gu, L.
History
DepositionAug 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
B: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
C: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
D: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
E: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
F: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
G: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
H: Putative gamma-hydroxymuconic semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)427,1828
Polymers427,1828
Non-polymers00
Water3,837213
1
A: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
C: Putative gamma-hydroxymuconic semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)106,7952
Polymers106,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-21 kcal/mol
Surface area31810 Å2
MethodPISA
2
B: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
F: Putative gamma-hydroxymuconic semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)106,7952
Polymers106,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-22 kcal/mol
Surface area31790 Å2
MethodPISA
3
D: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
G: Putative gamma-hydroxymuconic semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)106,7952
Polymers106,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-23 kcal/mol
Surface area32020 Å2
MethodPISA
4
E: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
H: Putative gamma-hydroxymuconic semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)106,7952
Polymers106,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-24 kcal/mol
Surface area31430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.531, 144.252, 138.288
Angle α, β, γ (deg.)90.00, 93.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 1:479 or resseq 481:487 )
21chain B and (resseq 1:479 or resseq 481:487 )
31chain C and (resseq 1:479 or resseq 481:487 )
41chain D and (resseq 1:479 or resseq 481:487 )
51chain E and (resseq 1:479 or resseq 481:487 )
61chain F and (resseq 1:479 or resseq 481:487 )
71chain G and (resseq 1:479 or resseq 481:487 )
81chain H and (resseq 1:479 or resseq 481:487 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 1:479 or resseq 481:487 )A1 - 479
121chain A and (resseq 1:479 or resseq 481:487 )A481 - 487
211chain B and (resseq 1:479 or resseq 481:487 )B1 - 479
221chain B and (resseq 1:479 or resseq 481:487 )B481 - 487
311chain C and (resseq 1:479 or resseq 481:487 )C1 - 479
321chain C and (resseq 1:479 or resseq 481:487 )C481 - 487
411chain D and (resseq 1:479 or resseq 481:487 )D1 - 479
421chain D and (resseq 1:479 or resseq 481:487 )D481 - 487
511chain E and (resseq 1:479 or resseq 481:487 )E1 - 479
521chain E and (resseq 1:479 or resseq 481:487 )E481 - 487
611chain F and (resseq 1:479 or resseq 481:487 )F1 - 479
621chain F and (resseq 1:479 or resseq 481:487 )F481 - 487
711chain G and (resseq 1:479 or resseq 481:487 )G1 - 479
721chain G and (resseq 1:479 or resseq 481:487 )G481 - 487
811chain H and (resseq 1:479 or resseq 481:487 )H1 - 479
821chain H and (resseq 1:479 or resseq 481:487 )H481 - 487

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Components

#1: Protein
Putative gamma-hydroxymuconic semialdehyde dehydrogenase


Mass: 53397.715 Da / Num. of mol.: 8 / Mutation: S426N, Y484H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Strain: WBC-3 / Gene: pnpE / Plasmid: pET-29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C1I208, aldehyde dehydrogenase (NAD+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 1.95 Å3/Da / Density % sol: 36.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2M potassium nitrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 86090 / Num. obs: 86090 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.7-2.83.40.3123.6192.2
5.81-503.80.05325.1199.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A4V

1a4v


Resolution: 2.704→41.684 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.38 / σ(F): 0 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 4166 4.99 %
Rwork0.2232 79335 -
obs0.2238 83501 93.52 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.763 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 171.1 Å2 / Biso mean: 42.8027 Å2 / Biso min: 6.84 Å2
Baniso -1Baniso -2Baniso -3
1-9.0882 Å2-0 Å28.5346 Å2
2---2.7664 Å20 Å2
3----6.3218 Å2
Refinement stepCycle: LAST / Resolution: 2.704→41.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29460 0 0 213 29673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0230084
X-RAY DIFFRACTIONf_angle_d1.49940808
X-RAY DIFFRACTIONf_dihedral_angle_d20.7410902
X-RAY DIFFRACTIONf_chiral_restr0.1044544
X-RAY DIFFRACTIONf_plane_restr0.015377
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3669X-RAY DIFFRACTIONPOSITIONAL0.635
12B3669X-RAY DIFFRACTIONPOSITIONAL0.635
13C3670X-RAY DIFFRACTIONPOSITIONAL0.808
14D3676X-RAY DIFFRACTIONPOSITIONAL0.685
15E3656X-RAY DIFFRACTIONPOSITIONAL0.643
16F3676X-RAY DIFFRACTIONPOSITIONAL0.717
17G3676X-RAY DIFFRACTIONPOSITIONAL0.756
18H3676X-RAY DIFFRACTIONPOSITIONAL0.735
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7039-2.73460.3381130.30892009212273
2.7346-2.76680.30591180.30782386250484
2.7668-2.80050.36311300.30312349247984
2.8005-2.8360.33331130.29162429254286
2.836-2.87330.30211380.28962492263087
2.8733-2.91260.29451250.2932459258488
2.9126-2.95420.33121260.28062513263989
2.9542-2.99830.27791300.26672519264989
2.9983-3.04510.26061170.25572522263990
3.0451-3.0950.29081430.24742609275291
3.095-3.14840.261470.25972541268891
3.1484-3.20560.29651430.25532615275893
3.2056-3.26730.25361250.24612629275493
3.2673-3.33390.26711340.24242676281094
3.3339-3.40640.27441340.23392654278895
3.4064-3.48560.24061410.22682709285095
3.4856-3.57270.23071550.2242667282296
3.5727-3.66920.2471350.22892755289097
3.6692-3.77720.23021290.21152775290498
3.7772-3.8990.20731620.20252761292398
3.899-4.03820.20821620.19992785294799
4.0382-4.19980.19661590.19722796295599
4.1998-4.39070.1791450.17892830297599
4.3907-4.62190.16241350.16552840297599
4.6219-4.91110.22061680.18842792296099
4.9111-5.28960.24281400.218528102950100
5.2896-5.82060.22531500.23712819296999
5.8206-6.65990.26881510.234128493000100
6.6599-8.37960.20321340.195828703004100
8.3796-41.68850.19851640.19652875303999
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)
10.0853-0.0283-0.16180.3467-0.11770.2823-0.04220.02790.01720.01490.0141-0.07840.00140.02740.01950.0582-0.0156-0.00610.069-0.00460.13-19.8671-14.6843-15.7567
20.36490.0231-0.15590.169-0.00930.5233-0.00260.01520.05280.11230.00930.07810.0376-0.0895-0.01080.17150.00320.05510.0806-0.00440.1582-16.54997.2539-66.2057
30.3938-0.1134-0.01930.2265-0.14170.52460.03950.01170.06460.0191-0.0248-0.01650.00520.0905-0.01450.0912-0.00820.04620.07110.00930.1316-16.992620.1509-10.6151
40.6976-0.1091-0.39620.4115-0.1150.2966-0.0002-0.09760.0316-0.04690.0604-0.0158-0.02590.0151-0.05160.0941-0.03720.01120.077-0.00490.0954-4.972474.2692-40.8066
50.34670.014-0.26640.10350.09210.5443-0.03790.06660.05050.00170.0383-0.03830.04010.0292-0.04490.0687-0.00490.01290.1357-0.0110.1365-37.212577.6731-18.3862
60.3846-0.2351-0.25390.030.11440.3352-0.1086-0.0424-0.13360.1831-0.03660.13270.2538-0.04020.06080.2753-0.00510.1131-0.0097-0.00690.1836-13.7079-27.2278-71.5866
70.76080.3306-0.39890.6673-0.33860.4091-0.13210.21520.071-0.22940.24390.17230.2969-0.2208-0.04290.2476-0.1439-0.03910.16720.05880.1304-18.474860.2884-70.4066
80.56310.0494-0.38250.14980.01220.34540.0157-0.2506-0.1165-0.0473-0.0122-0.1491-0.01690.1814-0.04320.1058-0.0061-0.02380.26130.04170.214-23.064573.363213.7003
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 487
2X-RAY DIFFRACTION2chain BB1 - 487
3X-RAY DIFFRACTION3chain CC1 - 487
4X-RAY DIFFRACTION4chain DD1 - 487
5X-RAY DIFFRACTION5chain EE1 - 485
6X-RAY DIFFRACTION6chain FF1 - 487
7X-RAY DIFFRACTION7chain GG1 - 487
8X-RAY DIFFRACTION8chain HH1 - 487

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