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- PDB-6b1b: STRUCTURE OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE (HPAB), OXYGE... -

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Basic information

Entry
Database: PDB / ID: 6b1b
TitleSTRUCTURE OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE (HPAB), OXYGENASE COMPONENT FROM ESCHERICHIA COLI MUTANT XS6 (APO Enzyme)
Components4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit
KeywordsOXIDOREDUCTASE / PROTEIN ENGINEERING: 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE / OXYGENASE COMPONENT / OXIDOREDUCTASE ACTIVE SITE LOOP MUTANT 7.2
Function / homology
Function and homology information


phenylacetate catabolic process / oxidoreductase activity, acting on the CH-CH group of donors / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / flavin adenine dinucleotide binding
Similarity search - Function
4-hydroxyphenylacetate 3-monooxygenase oxygenase component, gammaproteobacteria / 4-HPA 3-monooxygenase large component/Pyoverdin chromophore biosynthetic protein / HpaB/PvcC/4-BUDH / HpaB/PvcC/4-BUDH N-terminal / HpaB/PvcC/4-BUDH C-terminal / 4-hydroxyphenylacetate 3-hydroxylase C terminal / 4-hydroxyphenylacetate 3-hydroxylase N terminal / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
trimethylamine oxide / 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.944 Å
AuthorsZhou, D. / Kandavelu, P. / Wang, B.C. / Yan, Y. / Rose, J.P.
CitationJournal: Sci Rep / Year: 2019
Title: Structural Insights into Catalytic Versatility of the Flavin-dependent Hydroxylase (HpaB) from Escherichia coli.
Authors: Shen, X. / Zhou, D. / Lin, Y. / Wang, J. / Gao, S. / Kandavelu, P. / Zhang, H. / Zhang, R. / Wang, B.C. / Rose, J. / Yuan, Q. / Yan, Y.
History
DepositionSep 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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: 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit
B: 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,13810
Polymers119,5372
Non-polymers6018
Water19,1141061
1
A: 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit
B: 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit
hetero molecules

A: 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit
B: 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,27520
Polymers239,0734
Non-polymers1,20216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area34430 Å2
ΔGint-218 kcal/mol
Surface area60310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.455, 100.455, 336.435
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-1143-

HOH

21A-1161-

HOH

31A-1202-

HOH

41B-2523-

HOH

51B-2556-

HOH

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Components

#1: Protein 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit /


Mass: 59768.348 Da / Num. of mol.: 2 / Mutation: F208S, A211D, Q212L. V213G, M214S, E216S, N217D
Source method: isolated from a genetically manipulated source
Details: Active site loop mutant 7.2
Source: (gene. exp.) Escherichia coli (strain B / BL21-DE3) (bacteria)
Strain: B / BL21-DE3 / Gene: ECBD_3674 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140NG21
#2: Chemical
ChemComp-TMO / trimethylamine oxide / Trimethylamine N-oxide


Mass: 75.110 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C3H9NO
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1061 / 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: 3.66 Å3/Da / Density % sol: 66.42 %
Description: Crystal is a clear colorless prism measuring 80 BY 50 BY 10 microns
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROP VAPOR DIFFUSION AT 291K USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION AND A WELL SOLUTION CONTAINING 1.0 M SUCCINIC ACID, 0.1 M HEPES, AND 1% W/V ...Details: HANGING DROP VAPOR DIFFUSION AT 291K USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION AND A WELL SOLUTION CONTAINING 1.0 M SUCCINIC ACID, 0.1 M HEPES, AND 1% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 2,000 AT PH 7.0. CRYOPROTECTANT WAS MADE BY ADDING 30 % (V/V) GLYCEROL TO THE PRECIPITANT COCKTAIL.
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 8, 2017 / Details: ROSENBAUM ROCK
RadiationMonochromator: SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.944→46.36 Å / Num. obs: 127481 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 17.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 29.736
Reflection shellResolution: 1.944→1.98 Å / Redundancy: 16.8 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 8.449 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000V0.714data reduction
SCALEPACKV0.714data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UM5

5um5
PDB Unreleased entry


Resolution: 1.944→44.53 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 14.86
RfactorNum. reflection% reflection
Rfree0.1661 1999 1.57 %
Rwork0.1516 --
obs0.1518 127312 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.944→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8129 0 40 1061 9230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078353
X-RAY DIFFRACTIONf_angle_d0.93911325
X-RAY DIFFRACTIONf_dihedral_angle_d4.5374961
X-RAY DIFFRACTIONf_chiral_restr0.0541195
X-RAY DIFFRACTIONf_plane_restr0.0061473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9437-1.99230.20581390.17488676X-RAY DIFFRACTION99
1.9923-2.04620.19561410.16388827X-RAY DIFFRACTION100
2.0462-2.10640.19471410.15458852X-RAY DIFFRACTION100
2.1064-2.17440.17391400.15218832X-RAY DIFFRACTION100
2.1744-2.25210.17521420.14748855X-RAY DIFFRACTION100
2.2521-2.34230.16361420.14658877X-RAY DIFFRACTION100
2.3423-2.44890.17881420.15128913X-RAY DIFFRACTION100
2.4489-2.5780.17161420.15878890X-RAY DIFFRACTION100
2.578-2.73950.16771420.15288902X-RAY DIFFRACTION100
2.7395-2.9510.15621420.15248963X-RAY DIFFRACTION100
2.951-3.24790.15371440.14518976X-RAY DIFFRACTION100
3.2479-3.71760.14531440.13839044X-RAY DIFFRACTION100
3.7176-4.6830.161460.13519150X-RAY DIFFRACTION100
4.683-44.54130.16671520.17499556X-RAY DIFFRACTION100
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)
10.4047-0.14490.21220.4601-0.11841.2511-0.04150.1849-0.0082-0.40610.03050.15090.36930.23810.0159-0.0960.1570.18120.2604-0.0410.013542.7489-3.200714.7319
20.5254-0.0328-0.07310.4279-0.07260.44890.00330.10610.04760.0003-0.0412-0.0316-0.02970.12030.02690.060.01060.01170.20490.02610.093737.265512.034313.4538
30.54070.3-0.19830.6719-0.40230.7230.01810.010.09350.0618-0.0809-0.0652-0.06780.29360.04760.0654-0.00680.00790.25390.02650.14447.360412.725224.1376
40.3192-0.30740.10740.7683-0.12240.5257-0.00620.045-0.0220.1070.01890.06560.08470.00350.00290.0770.00990.00680.0858-0.00550.082119.35810.939529.8882
50.7138-0.38960.45412.44540.82220.8631-0.08190.02670.1264-0.07490.0083-0.03330.01810.08540.05490.10160.02960.00680.08820.00540.066727.13-1.627234.5746
60.7002-0.2059-0.0810.58990.0260.4817-0.05460.09370.11510.0317-0.018-0.0487-0.2221-0.03160.01130.18250.0179-0.03590.0750.00960.09116.816940.617229.9261
70.3931-0.1378-0.00260.40070.27140.901-0.04620.06950.0298-0.0183-0.01390.0294-0.1259-0.22320.03020.06630.0376-0.0290.16450.00280.0882-10.682326.852116.2268
80.57230.31960.31130.63560.44380.87720.0074-0.045-0.09160.1005-0.05590.06330.0724-0.31690.03660.0651-0.00460.00280.22730.00250.1373-17.877518.682326.57
90.50050.06850.0890.77020.2220.8470.01460.0205-0.00050.09420.0094-0.0446-0.024-0.0165-0.01490.04470.0115-0.01060.0630.01330.075210.911823.336826.5847
100.67780.37790.00621.53250.33190.6427-0.0139-0.0004-0.04020.08650.0373-0.0764-0.14150.04290.00080.17910.0287-0.02170.06660.0110.08536.039841.56340.3194
110.6214-0.12910.12170.5882-0.14870.4709-0.02290.0794-0.0822-0.0082-0.01070.03660.21230.04550.00820.15550.02430.01890.0934-0.01580.080622.4178-8.819627.3731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 71 )
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 167 )
3X-RAY DIFFRACTION3chain 'A' and (resid 168 through 300 )
4X-RAY DIFFRACTION4chain 'A' and (resid 301 through 431 )
5X-RAY DIFFRACTION5chain 'A' and (resid 432 through 464 )
6X-RAY DIFFRACTION6chain 'A' and (resid 465 through 520 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 166 )
8X-RAY DIFFRACTION8chain 'B' and (resid 167 through 300 )
9X-RAY DIFFRACTION9chain 'B' and (resid 301 through 396 )
10X-RAY DIFFRACTION10chain 'B' and (resid 397 through 464 )
11X-RAY DIFFRACTION11chain 'B' and (resid 465 through 519 )

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