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- PDB-6qyh: Structure of Apo HPAB from E.coli -

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Basic information

Entry
Database: PDB / ID: 6qyh
TitleStructure of Apo HPAB from E.coli
Components4-hydroxyphenylacetate 3-monooxygenase oxygenase component
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE MONOOXYGENASE
Function / homology
Function and homology information


4-hydroxyphenylacetate 3-monooxygenase / 4-hydroxyphenylacetate 3-monooxygenase activity / phenylacetate catabolic process / oxidoreductase activity, acting on the CH-CH group of donors / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 4-hydroxyphenylacetate 3-monooxygenase oxygenase component / 4-hydroxyphenylacetate 3-monooxygenase oxygenase component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsPecqueur, L. / Lombard, M. / Deng, Y. / Fontecave, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency53311-LABX-0011 France
CitationJournal: Chembiochem / Year: 2020
Title: Structural and Functional Characterization of 4-Hydroxyphenylacetate 3-Hydroxylase from Escherichia coli.
Authors: Deng, Y. / Faivre, B. / Back, O. / Lombard, M. / Pecqueur, L. / Fontecave, M.
History
DepositionMar 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Data collection / Database references / Category: citation / reflns_shell
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _reflns_shell.d_res_high / _reflns_shell.d_res_low
Revision 1.2Jan 24, 2024Group: 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 / struct_conn
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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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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 component
B: 4-hydroxyphenylacetate 3-monooxygenase oxygenase component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,62117
Polymers117,9192
Non-polymers1,70215
Water9,044502
1
A: 4-hydroxyphenylacetate 3-monooxygenase oxygenase component
B: 4-hydroxyphenylacetate 3-monooxygenase oxygenase component
hetero molecules

A: 4-hydroxyphenylacetate 3-monooxygenase oxygenase component
B: 4-hydroxyphenylacetate 3-monooxygenase oxygenase component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,24334
Polymers235,8394
Non-polymers3,40430
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_654-x+y+1,y,-z-1/21
Buried area40890 Å2
ΔGint-196 kcal/mol
Surface area60770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.280, 189.280, 163.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-514-

MET

21B-514-

MET

31A-708-

HOH

41A-790-

HOH

51A-954-

HOH

61B-842-

HOH

71B-925-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 4-hydroxyphenylacetate 3-monooxygenase oxygenase component / 4-hydroxyphenylacetate 3-monooxygenase / oxygenase component


Mass: 58959.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: hpaB, CR538_21835, DS732_04180, NCTC9045_04991, NCTC9117_05338
Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3
References: UniProt: A0A2G8ZEZ1, UniProt: Q57160*PLUS, 4-hydroxyphenylacetate 3-monooxygenase

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Non-polymers , 5 types, 517 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 3.59 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES 0.1M pH 7.5 PEG 400 30% (w/v) CaCl2 0.2M MgCl2 0.1M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.94→49.4 Å / Num. obs: 127313 / % possible obs: 99.88 % / Redundancy: 26.13 % / Biso Wilson estimate: 42.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.032 / Rrim(I) all: 0.164 / Net I/σ(I): 13.3
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 25.84 % / Rmerge(I) obs: 3.41 / Mean I/σ(I) obs: 1 / Num. unique obs: 12389 / CC1/2: 0.472 / Rpim(I) all: 0.677 / Rrim(I) all: 3.478 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4oo2

4oo2


Resolution: 1.94→19.45 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.101 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.094
RfactorNum. reflection% reflectionSelection details
Rfree0.184 2217 1.74 %RANDOM
Rwork0.166 ---
obs0.167 127155 100 %-
Displacement parametersBiso mean: 47.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.4287 Å20 Å20 Å2
2---1.4287 Å20 Å2
3---2.8574 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 1.94→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8059 0 107 502 8668
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018503HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9611520HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2961SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1464HARMONIC5
X-RAY DIFFRACTIONt_it8503HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion17.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1069SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance20HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10605SEMIHARMONIC4
LS refinement shellResolution: 1.94→1.95 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2843 -1.85 %
Rwork0.2709 2497 -
all0.2712 2544 -
obs--99.12 %
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)
10.11850.1017-0.03120.79370.07880.40690.0546-0.0157-0.01970.1922-0.06720.09910.0615-0.05410.01260.066-0.02490.0078-0.04370.01070.000689.6904-23.5247-22.2493
20.1215-0.06680.0531.3163-0.2890.3856-0.0004-0.02170.01280.2998-0.0381-0.2221-0.16230.07620.03850.1275-0.0323-0.0329-0.0335-0.00690.0074105.34279.1159-24.8592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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