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- PDB-4go4: Crystal structure of PnpE in complex with Nicotinamide adenine di... -

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Basic information

Entry
Database: PDB / ID: 4go4
TitleCrystal structure of PnpE in complex with Nicotinamide adenine dinucleotide
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 / organic substance metabolic process / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Putative gamma-hydroxymuconic semialdehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.099 Å
AuthorsSu, J. / Zhang, C. / Liu, S. / Zhu, D. / Gu, L.
CitationJournal: To be Published
Title: Crystal structure of PnpE in complex with Nicotinamide adenine dinucleotide
Authors: Su, J. / Zhang, C. / Liu, S. / Zhu, D. / Gu, L.
History
DepositionAug 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)432,68116
Polymers427,3748
Non-polymers5,3078
Water2,432135
1
A: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
B: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1704
Polymers106,8442
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-41 kcal/mol
Surface area31810 Å2
MethodPISA
2
C: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
D: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1704
Polymers106,8442
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8680 Å2
ΔGint-39 kcal/mol
Surface area31670 Å2
MethodPISA
3
E: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
F: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1704
Polymers106,8442
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-41 kcal/mol
Surface area31520 Å2
MethodPISA
4
G: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
H: Putative gamma-hydroxymuconic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1704
Polymers106,8442
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8820 Å2
ΔGint-41 kcal/mol
Surface area31720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.911, 154.539, 143.435
Angle α, β, γ (deg.)90.00, 95.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative gamma-hydroxymuconic semialdehyde dehydrogenase


Mass: 53421.758 Da / Num. of mol.: 8 / Mutation: S426H, Y484H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (bacteria) / Strain: WBC-3 / Gene: pnpE / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C1I208, aldehyde dehydrogenase (NAD+)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M BICINE pH 8.5, 20% PEG 10000, 1mM NAD, 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: May 10, 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: 3→50 Å / Num. all: 69131 / Num. obs: 69131 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 62.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3-3.113.30.6032184.8
6.46-503.70.02845.3199.5

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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: 4GO3

4go3


Resolution: 3.099→37.243 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.38 / σ(F): 0 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 1759 2.9 %
Rwork0.2067 --
obs0.208 60632 88.61 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10.933 Å2 / ksol: 0.289 e/Å3
Displacement parametersBiso max: 153.48 Å2 / Biso mean: 60.26 Å2 / Biso min: 12.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.2112 Å20 Å2-2.3687 Å2
2--9.8381 Å2-0 Å2
3----10.0493 Å2
Refinement stepCycle: LAST / Resolution: 3.099→37.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29496 0 352 135 29983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01130592
X-RAY DIFFRACTIONf_angle_d1.55541560
X-RAY DIFFRACTIONf_dihedral_angle_d20.35811536
X-RAY DIFFRACTIONf_chiral_restr0.0864616
X-RAY DIFFRACTIONf_plane_restr0.0055416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0994-3.18310.41381070.30433669377672
3.1831-3.27670.36371190.29983881400076
3.2767-3.38240.32311200.28043999411979
3.3824-3.50320.31011230.26114142426581
3.5032-3.64340.29781300.24554275440584
3.6434-3.8090.29811290.23124369449886
3.809-4.00960.25461340.21644518465288
4.0096-4.26050.23681410.19954668480992
4.2605-4.58890.2021490.17254976512597
4.5889-5.04970.22861480.17415005515398
5.0497-5.77810.25311530.19795083523699
5.7781-7.27090.2241520.17785123527599
7.2709-37.24570.19881540.17925165531999

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