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- PDB-4u3w: X-ray crystal structure of 2-aminomuconate 6-semialdehyde dehydro... -

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Basic information

Entry
Database: PDB / ID: 4u3w
TitleX-ray crystal structure of 2-aminomuconate 6-semialdehyde dehydrogenase from Burkholderia cenocepacia
Components2-aminomuconate 6-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase aminomuconate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / metal ion binding
Similarity search - Function
2-hydroxymuconic semialdehyde dehydrogenase / 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, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain ...2-hydroxymuconic semialdehyde dehydrogenase / 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, 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-aminomuconate 6-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9501 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: X-ray crystal structure of 2-aminomuconate 6-semialdehyde dehydrogenase from Burkholderia cenocepacia
Authors: Fairman, J.W. / Dranow, D.M. / Lorimer, D. / Edwards, T.E.
History
DepositionJul 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_high / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)109,0659
Polymers108,8572
Non-polymers2087
Water13,169731
1
A: 2-aminomuconate 6-semialdehyde dehydrogenase
B: 2-aminomuconate 6-semialdehyde dehydrogenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)218,12918
Polymers217,7134
Non-polymers41614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area16840 Å2
ΔGint-156 kcal/mol
Surface area61550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.750, 87.690, 111.880
Angle α, β, γ (deg.)90.000, 128.310, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ALA / End label comp-ID: ALA

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ARGARGchain AAA12 - 49621 - 505
2GLNGLNchain BBB13 - 49622 - 505

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Components

#1: Protein 2-aminomuconate 6-semialdehyde dehydrogenase


Mass: 54428.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: nbaE, BCAM2132 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EFS9
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 731 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus well A6 - 0.1M MOPS/HEPES-Na pH 7.5, 10% PEG 8000, 20% ethylene glycol, 0.03 M magnesium chloride, 0.3 M calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 9, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 89287 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.47 % / Biso Wilson estimate: 30.07 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.065 / Χ2: 1.002 / Net I/σ(I): 15.2 / Num. measured all: 399625
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.95-24.540.860.5392.6829946660865840.61299.6
2-2.060.9160.3973.629159644764250.45199.7
2.06-2.120.950.3134.5428192623162140.35699.7
2.12-2.180.9580.2615.5327469607560540.29799.7
2.18-2.250.9760.2036.9426653590158760.23199.6
2.25-2.330.9810.1678.3725716569356760.1999.7
2.33-2.420.9880.13410.324858551854940.15399.6
2.42-2.520.990.11611.6323742528052590.13299.6
2.52-2.630.9910.0961423019512951040.1199.5
2.63-2.760.9940.0816.1921617483448260.09199.8
2.76-2.910.9950.06918.6520647464646180.07899.4
2.91-3.080.9960.05822.319428439043710.06699.6
3.08-3.30.9970.04925.4618113414441200.05699.4
3.3-3.560.9970.04428.7116550381438020.0599.7
3.56-3.90.9980.03931.3315318354035200.04599.4
3.9-4.360.9980.03733.3713989322732110.04299.5
4.36-5.030.9980.03335.112339283928220.03899.4
5.03-6.170.9980.03334.2610682244424250.03899.2
6.17-8.720.9980.03135.268099186818550.03599.3
8.720.9980.03354089107910310.03495.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
XDSdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: dev_1738)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E4G

4e4g


Resolution: 1.9501→43.845 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 4394 4.92 %RANDOM
Rwork0.1657 84864 --
obs0.1675 89258 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.87 Å2 / Biso mean: 38.5573 Å2 / Biso min: 18.12 Å2
Refinement stepCycle: final / Resolution: 1.9501→43.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7272 0 10 731 8013
Biso mean--44.11 44.14 -
Num. residues----969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0187557
X-RAY DIFFRACTIONf_angle_d1.46110323
X-RAY DIFFRACTIONf_chiral_restr0.0811174
X-RAY DIFFRACTIONf_plane_restr0.0081365
X-RAY DIFFRACTIONf_dihedral_angle_d12.6022685
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4150X-RAY DIFFRACTION4.715TORSIONAL
12B4150X-RAY DIFFRACTION4.715TORSIONAL
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 (%)
1.9501-1.97220.27321370.242228412978100
1.9722-1.99540.3281300.229728052935100
1.9954-2.01980.25131300.214328352965100
2.0198-2.04530.23421460.21128272973100
2.0453-2.07230.26491610.206527692930100
2.0723-2.10060.22631380.200928342972100
2.1006-2.13070.25841420.19828212963100
2.1307-2.16250.2651680.194227922960100
2.1625-2.19620.22741360.191528462982100
2.1962-2.23230.25711340.179728282962100
2.2323-2.27070.22471660.178227882954100
2.2707-2.3120.21891470.170228432990100
2.312-2.35650.20141400.163428072947100
2.3565-2.40460.20461630.159428142977100
2.4046-2.45690.19771460.171328142960100
2.4569-2.5140.23281360.16628152951100
2.514-2.57690.2231370.164228352972100
2.5769-2.64660.21151410.161928382979100
2.6466-2.72440.21181670.169428092976100
2.7244-2.81230.22381610.174128132974100
2.8123-2.91280.21371400.179628322972100
2.9128-3.02940.23591280.1828632991100
3.0294-3.16730.2261520.176828352987100
3.1673-3.33420.21011480.176928072955100
3.3342-3.5430.22391640.173528493013100
3.543-3.81640.20041430.163328252968100
3.8164-4.20020.15651520.144228483000100
4.2002-4.80730.15351560.125828463002100
4.8073-6.05420.15571380.145828783016100
6.0542-43.85610.16461470.15312907305499
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)
10.74640.365-0.23771.15560.51612.0716-0.07020.0007-0.0582-0.0761-0.05690.1962-0.2407-0.4497-0.04160.22580.0969-0.02160.2674-0.07950.20253.11612.808214.4547
21.2041-0.9871-0.68880.99170.60770.4823-0.00860.02920.0112-0.02750.0243-0.0187-0.17010.0381-0.00180.32720.0484-0.00580.3305-0.0350.28852.37111.710726.5069
30.8835-0.2881-0.28011.72471.00991.79830.04160.01150.0853-0.28570.1768-0.1093-0.36310.4576-0.13410.2546-0.10470.04540.4101-0.0390.237979.682718.948931.1291
42.0912-0.7470.7773-0.4888-0.2253-0.2880.06610.01310.1553-0.08520.0563-0.0923-0.30710.1452-0.1130.5030.01570.06110.545-0.04540.452752.548624.655732.8908
52.2868-0.23880.81821.3332-0.35361.0579-0.7577-0.0960.66860.23940.1495-0.4053-1.1220.3378-0.42020.4141-0.2665-0.07730.1990.11940.339154.517556.35621.7215
61.2459-0.84240.99110.813-0.63781.8959-0.186-0.09320.03170.07820.13550.0168-0.1953-0.15390.1030.2972-0.0939-0.00690.2591-0.00810.251950.912544.286830.2576
72.07270.74980.84450.37050.21580.3194-0.13590.2482-0.1269-0.09290.0996-0.2312-0.18090.28070.03080.3822-0.01660.01110.43370.04860.381845.296640.752817.1254
81.07680.13930.40940.94360.0152.039-0.1571-0.05790.0067-0.07750.0513-0.0018-0.06840.05710.09320.18060.07430.01660.15650.03140.155226.015938.913111.7089
93.8368-1.62232.3628-0.3153-0.75050.705-0.107-0.01340.034-0.01870.127-0.0229-0.157-0.10360.04230.4989-0.0449-0.01480.49720.03810.418247.959633.455431.3663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 71 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 252 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 253 through 453 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 454 through 496 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 13 through 101 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 102 through 206 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 207 through 299 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 300 through 453 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 454 through 496 )B0

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