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- PDB-6pxs: Crystal structure of iminodiacetate oxidase (IdaA) from Chelativo... -

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Basic information

Entry
Database: PDB / ID: 6pxs
TitleCrystal structure of iminodiacetate oxidase (IdaA) from Chelativorans sp. BNC1
ComponentsFAD dependent oxidoreductase
KeywordsOXIDOREDUCTASE / iminodiacetate / oxidase / bioredmediation / EDTA / chelativorans
Function / homologyFAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / nucleotide binding / cytoplasm / FLAVIN-ADENINE DINUCLEOTIDE / FAD dependent oxidoreductase
Function and homology information
Biological speciesChelativorans sp. BNC1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.836 Å
AuthorsJun, S.Y. / Lewis, K.M. / Xun, L. / Kang, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 1804699 United States
National Science Foundation (NSF, United States)DBI 0959778 United States
CitationJournal: Mol.Microbiol. / Year: 2019
Title: Structural and biochemical characterization of iminodiacetate oxidase from Chelativorans sp. BNC1.
Authors: Kang, C. / Jun, S.Y. / Bravo, A.G. / Vargas, E.M. / Liu, H. / Lewis, K.M. / Xun, L.
History
DepositionJul 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAD dependent oxidoreductase
B: FAD dependent oxidoreductase
C: FAD dependent oxidoreductase
D: FAD dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,7058
Polymers160,5634
Non-polymers3,1424
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13860 Å2
ΔGint-65 kcal/mol
Surface area51360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.457, 113.457, 266.119
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein
FAD dependent oxidoreductase


Mass: 40140.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chelativorans sp. BNC1 (bacteria) / Strain: BNC1 / Gene: Meso_1828 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q11HA4
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M tris pH 8.5, 0.2 M trimethylamine N-oxide dihydrate, 20% (w/v) PEG MME 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 43608 / % possible obs: 99.8 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.479 / Rpim(I) all: 0.137 / Rrim(I) all: 0.499 / Χ2: 1.025 / Net I/σ(I): 2.7 / Num. measured all: 548682
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.8545.98520660.0443.1996.8340.86496.2
2.85-2.95.85.73121160.1072.516.280.89699.5
2.9-2.967.85.17521430.1551.9245.5330.938100
2.96-3.029.74.17521310.2771.3894.4060.959100
3.02-3.0811.73.53421560.3381.0693.6940.992100
3.08-3.1513.12.83621430.4430.8092.950.995100
3.15-3.2314.11.92821490.5450.52921.069100
3.23-3.3214.51.58321540.6690.4281.641.078100
3.32-3.4214.61.23121510.7450.3331.2751.083100
3.42-3.5314.51.01621720.840.2751.0531.09100
3.53-3.6514.50.78921710.8890.2140.8171.133100
3.65-3.814.50.68221520.9260.1850.7071.201100
3.8-3.9714.40.5621630.9590.1520.5811.054100
3.97-4.1814.40.39821930.9870.1080.4121.037100
4.18-4.4414.30.31321890.9820.0860.3240.901100
4.44-4.7914.20.23321990.9910.0640.2421.043100
4.79-5.2714.10.2222060.9920.060.2280.973100
5.27-6.0313.60.24322430.9880.0680.2521.008100
6.03-7.5913.80.16622770.9950.0460.1730.956100
7.59-5013.20.05524340.9990.0160.0570.939100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RYI

1ryi


Resolution: 2.836→49.842 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 1952 4.75 %
Rwork0.2175 39142 -
obs0.2191 41094 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.26 Å2 / Biso mean: 67.5283 Å2 / Biso min: 14 Å2
Refinement stepCycle: final / Resolution: 2.836→49.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10864 0 336 30 11230
Biso mean--51.47 47.5 -
Num. residues----1478
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.836-2.9070.3973940.4134196470
2.907-2.98550.3831390.3852272197
2.9855-3.07340.35561400.33342798100
3.0734-3.17260.36081390.31782807100
3.1726-3.28590.35091400.28672816100
3.2859-3.41750.26191410.26422826100
3.4175-3.5730.28411420.23442846100
3.573-3.76130.26091400.23212820100
3.7613-3.99680.26931430.20932838100
3.9968-4.30530.20571430.1822868100
4.3053-4.73820.21211440.16382889100
4.7382-5.42320.20141440.16762886100
5.4232-6.82980.24621470.20372942100
6.8298-49.8420.1931560.17813121100
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)
11.0145-0.6170.9252.1982-0.89281.6539-0.04820.0442-0.09320.01480.12550.11950.2412-0.1754-00.3594-0.07520.01960.3556-0.03480.29345.1244-19.4317.1384
20.05320.02930.22231.9394-0.37110.95910.01190.186-0.08870.01850.1026-0.20430.1644-0.04310.00660.3394-0.0238-0.00780.3091-0.05950.297453.9524-18.515.8443
30.5199-0.4957-0.65451.4214-0.1651.26470.11150.0565-0.0316-0.00840.14430.3312-0.011-0.29270.21460.345-0.00320.02250.40730.09130.444435.08246.732329.7182
40.7608-1.25510.16172.5074-0.42491.22930.0602-0.09630.08450.27450.06830.0341-0.1726-0.18030.00220.34230.01030.07670.3384-0.00370.323943.701712.802129.8321
51.16650.0032-0.53762.18750.65781.7878-0.03440.00510.06470.03790.1219-0.4053-0.23620.46250.00080.298-0.0911-0.06490.35070.04910.316674.708724.29217.2502
60.80560.5144-0.07672.16410.31990.5434-0.01540.0770.06230.04920.0664-0.077-0.1280.109-00.3714-0.048-0.0630.32040.03910.323965.078524.04447.762
70.2038-0.32720.24181.37630.37380.93290.0085-0.05270.20460.0175-0.1172-0.563-0.09650.260700.383-0.0384-0.07370.44220.09050.805187.0258-7.723932.5856
80.9799-0.8471-0.27513.36790.8730.22160.1245-0.03080.01640.0784-0.1333-0.45740.07120.1002-00.38040.0124-0.05460.29720.10610.356577.9736-17.072828.0175
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 192)A1 - 192
2X-RAY DIFFRACTION2(chain 'A' and resid 193 through 370)A193 - 370
3X-RAY DIFFRACTION3(chain 'B' and resid 1 through 185)B1 - 185
4X-RAY DIFFRACTION4(chain 'B' and resid 186 through 370)B186 - 370
5X-RAY DIFFRACTION5(chain 'C' and resid 2 through 187)C2 - 187
6X-RAY DIFFRACTION6(chain 'C' and resid 188 through 370)C188 - 370
7X-RAY DIFFRACTION7(chain 'D' and resid 2 through 170)D2 - 170
8X-RAY DIFFRACTION8(chain 'D' and resid 171 through 370)D171 - 370

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