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- PDB-7bzv: Crystal structure of 2-aminomuconic 6-semialdehyde dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 7bzv
TitleCrystal structure of 2-aminomuconic 6-semialdehyde dehydrogenase from Pseudomonas species AP-3
Components2-aminomuconic 6-semialdehyde dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / meta-cleavage pathway for 2-aminophenol catabolism. 2-aminomuconic 6-semialdehyde dehydrogenase
Function / homology
Function and homology information


aminomuconate-semialdehyde dehydrogenase / aminomuconate-semialdehyde dehydrogenase activity / :
Similarity search - Function
2-hydroxymuconic semialdehyde dehydrogenase / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / 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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 2-aminomuconic 6-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.988 Å
AuthorsShi, Q.L. / Chen, Y.J. / Su, D.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0505903 China
CitationJournal: Environ.Microbiol. / Year: 2021
Title: The tetrameric assembly of 2-aminomuconic 6-semialdehyde dehydrogenase is a functional requirement of cofactor NAD + binding.
Authors: Shi, Q. / Chen, Y. / Li, X. / Dong, H. / Chen, C. / Zhong, Z. / Yang, C. / Liu, G. / Su, D.
History
DepositionApr 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Jun 19, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-aminomuconic 6-semialdehyde dehydrogenase
B: 2-aminomuconic 6-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,64511
Polymers107,7422
Non-polymers9039
Water13,331740
1
A: 2-aminomuconic 6-semialdehyde dehydrogenase
B: 2-aminomuconic 6-semialdehyde dehydrogenase
hetero molecules

A: 2-aminomuconic 6-semialdehyde dehydrogenase
B: 2-aminomuconic 6-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,29022
Polymers215,4844
Non-polymers1,80618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area22350 Å2
ΔGint-70 kcal/mol
Surface area61220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.526, 181.526, 181.157
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-737-

HOH

21B-793-

HOH

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Components

#1: Protein 2-aminomuconic 6-semialdehyde dehydrogenase / Aminomuconate-semialdehyde dehydrogenase


Mass: 53871.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: amnC / Production host: Escherichia coli (E. coli)
References: UniProt: Q9KWS5, aminomuconate-semialdehyde dehydrogenase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.92 Å3/Da / Density % sol: 69.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: ammonium sulfate, BIS-TRIS, Polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Sep 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.988→50 Å / Num. obs: 120102 / % possible obs: 100 % / Redundancy: 18.8 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.02 / Rrim(I) all: 0.088 / Χ2: 0.56 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.99-2.0218.10.83959040.8820.2010.8630.42
2.02-2.0619.20.71259200.9210.1660.7310.417
2.06-2.119.50.60859240.9450.140.6240.434
2.1-2.1419.40.51659170.9580.1190.5290.423
2.14-2.1919.20.41759460.9710.0970.4290.426
2.19-2.2418.90.34759140.980.0810.3560.432
2.24-2.317.60.30459690.9820.0740.3130.45
2.3-2.3618.40.24259320.990.0580.2480.445
2.36-2.4319.90.20759390.9930.0470.2130.451
2.43-2.5119.80.18459690.9940.0420.1890.457
2.51-2.619.50.15659760.9960.0360.160.477
2.6-2.718.90.13859620.9970.0320.1410.493
2.7-2.8217.20.11859840.9970.0290.1210.512
2.82-2.9719.60.09759960.9980.0220.10.547
2.97-3.1619.80.08160000.9990.0180.0830.616
3.16-3.419.40.06860400.9990.0160.0690.707
3.4-3.7417.50.05860670.9990.0140.060.822
3.74-4.2919.90.05260940.9990.0120.0540.972
4.29-5.418.10.04761670.9990.0110.0480.962
5.4-5017.30.03964820.9990.010.040.713

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NPI

4npi


Resolution: 1.988→25.536 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2075 6085 5.07 %
Rwork0.1719 113835 -
obs0.1737 119920 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.03 Å2 / Biso mean: 43.3202 Å2 / Biso min: 16.55 Å2
Refinement stepCycle: final / Resolution: 1.988→25.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7535 0 127 740 8402
Biso mean--81.79 44.46 -
Num. residues----979
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.988-2.01060.31930.2573354895
2.0106-2.03430.25022000.22793777100
2.0343-2.05910.26421990.21663739100
2.0591-2.08510.25752170.21053758100
2.0851-2.11250.23771990.19963739100
2.1125-2.14150.20312000.19083744100
2.1415-2.1720.23492200.1893753100
2.172-2.20440.23232010.18993747100
2.2044-2.23890.21332160.18773738100
2.2389-2.27550.22932070.18753753100
2.2755-2.31480.21671970.18193767100
2.3148-2.35680.21722170.16753770100
2.3568-2.40210.21361820.16743775100
2.4021-2.45110.21732020.17263781100
2.4511-2.50440.20451990.16753756100
2.5044-2.56260.18342060.17053794100
2.5626-2.62660.23112040.17123773100
2.6266-2.69750.23112240.17853759100
2.6975-2.77680.24081790.1793810100
2.7768-2.86630.21672060.18483788100
2.8663-2.96860.22531810.18313824100
2.9686-3.08730.23121950.17573827100
3.0873-3.22760.19221760.17523810100
3.2276-3.39740.21012440.1723794100
3.3974-3.60970.19252070.16833849100
3.6097-3.88750.19951940.15363848100
3.8875-4.2770.17022110.14243871100
4.277-4.89220.16091930.12643903100
4.8922-6.14940.19571920.17183948100
6.1494-25.5360.22212240.2009409299
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)
10.3418-0.4023-0.09640.5496-0.29990.9565-0.1728-0.12230.27780.23550.1862-0.21940.5402-0.0037-0.10350.24980.0584-0.05460.35080.1090.270339.03455.341107.817
20.54280.0144-0.73850.0198-0.01991.2530.0199-0.04280.10230.02070.0859-0.04230.05-0.08510.00520.10770.0262-0.03680.25570.08360.232740.61264.51495.64
30.5731-0.0788-0.22131.0434-0.19910.49280.0156-0.2775-0.02790.15990.07120.0232-0.1099-0.0678-00.16190.03740.02080.43580.05210.194118.00683.138101.037
40.5455-0.1171-0.018-0.0222-0.03670.15070.0065-0.1818-0.08740.03880.0685-0.0033-0.0004-0.017900.16310.0057-0.00030.27530.00950.237139.9981.33687.34
50.214-0.1210.29550.0721-0.16950.4303-0.4031-0.24550.31720.17770.2018-0.0682-0.72380.0037-0.1650.62010.0522-0.31990.3223-0.50710.562965.53107.574103.741
61.2592-0.14170.71940.3371-0.24580.8653-0.1718-0.10710.15570.08770.0948-0.045-0.30370.0092-0.00090.1736-0.00230.00040.2083-0.09480.220557.90795.93391.686
70.3439-0.01880.17750.5786-0.42540.4592-0.021-0.21270.11590.1321-0.01510.0018-0.09510.0182-0.00270.1641-0.0157-0.02170.4032-0.04830.278674.36478.89195.365
80.5982-0.44210.30090.6616-0.28740.309-0.038-0.25370.00660.2204-0.022-0.01780.05360.0284-0.0130.2012-0.0301-0.02260.399100.194177.55172.35199.247
90.301-0.0179-0.3273-0.014-0.06850.27620.0057-0.1563-0.00070.03640.0875-0.03280.00770.02030.00220.21090.01710.01050.3015-0.00990.270249.42881.16185.771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:60 )A0 - 60
2X-RAY DIFFRACTION2( CHAIN A AND RESID 61:245 )A61 - 245
3X-RAY DIFFRACTION3( CHAIN A AND RESID 246:409 )A246 - 409
4X-RAY DIFFRACTION4( CHAIN A AND RESID 410:488 )A410 - 488
5X-RAY DIFFRACTION5( CHAIN B AND RESID 0:22 )B0 - 22
6X-RAY DIFFRACTION6( CHAIN B AND RESID 23:219 )B23 - 219
7X-RAY DIFFRACTION7( CHAIN B AND RESID 220:330 )B220 - 330
8X-RAY DIFFRACTION8( CHAIN B AND RESID 331:442 )B331 - 442
9X-RAY DIFFRACTION9( CHAIN B AND RESID 443:489 )B443 - 489

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