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- PDB-3egr: CRYSTAL STRUCTURE OF A PHENYLACETATE-COA OXYGENASE SUBUNIT PAAB (... -

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Basic information

Entry
Database: PDB / ID: 3egr
TitleCRYSTAL STRUCTURE OF A PHENYLACETATE-COA OXYGENASE SUBUNIT PAAB (REUT_A2307) FROM RALSTONIA EUTROPHA JMP134 AT 2.65 A RESOLUTION
Componentsphenylacetate-CoA oxygenase subunit PaaB
KeywordsOXIDOREDUCTASE / PHENYLACETATE-COA OXYGENASE SUBUNIT PAAB / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyPhenylacetic acid degradation B / Phenylacetic acid degradation B / Phenylacetyl-CoA epoxidase, subunit B / Phenylacetic acid degradation B / Ubiquitin-like (UB roll) / Roll / Alpha Beta / THIOCYANATE ION / Phenylacetic acid degradation B
Function and homology information
Biological speciesRalstonia eutropha JMP134 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of phenylacetate-CoA oxygenase subunit PaaB (YP_297411.1) from RALSTONIA EUTROPHA JMP134 at 2.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_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_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: phenylacetate-CoA oxygenase subunit PaaB
B: phenylacetate-CoA oxygenase subunit PaaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7284
Polymers22,6122
Non-polymers1162
Water1,04558
1
A: phenylacetate-CoA oxygenase subunit PaaB
B: phenylacetate-CoA oxygenase subunit PaaB
hetero molecules

A: phenylacetate-CoA oxygenase subunit PaaB
B: phenylacetate-CoA oxygenase subunit PaaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4578
Polymers45,2254
Non-polymers2324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area5430 Å2
ΔGint-46 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.260, 93.260, 114.698
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-152-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSALAALA5AA4 - 355 - 36
21LYSLYSALAALA5BB4 - 355 - 36
12LEULEUPROPRO6AA36 - 6537 - 66
22LEULEUPROPRO6BB36 - 6537 - 66

NCS ensembles :
ID
1
2

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Components

#1: Protein phenylacetate-CoA oxygenase subunit PaaB / Phenylacetic acid degradation B


Mass: 11306.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha JMP134 (bacteria) / Gene: YP_297411.1, Reut_A3207 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q46WB6
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.18 Å3/Da / Density % sol: 61.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2000M KThioCyanate, 20.0000% PEG-3350, No Buffer pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97966, 0.97951
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 26, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979661
30.979511
ReflectionResolution: 2.65→29.566 Å / Num. obs: 9062 / % possible obs: 99.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 52.835 Å2 / Rmerge(I) obs: 0.155 / Rsym value: 0.155 / Net I/σ(I): 15.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.65-2.7210.70.8093.169046450.809100
2.72-2.7910.60.6393.967186330.639100
2.79-2.8710.70.527565846140.527100
2.87-2.9610.80.455.664546000.45100
2.96-3.0610.70.361762485850.361100
3.06-3.1710.60.2868.859805640.286100
3.17-3.2910.60.2410.358355490.24100
3.29-3.4210.60.19412.856005290.194100
3.42-3.5710.50.1661553325070.166100
3.57-3.7510.50.12620.351604920.126100
3.75-3.9510.40.12420.948514650.124100
3.95-4.1910.40.10624.546314440.106100
4.19-4.4810.30.08929.243864270.089100
4.48-4.8410.20.08629.740013920.086100
4.84-5.310.20.09228.637053650.092100
5.3-5.93100.09724.734283430.097100
5.93-6.849.80.09924.629673030.099100
6.84-8.389.50.07532.424842610.075100
8.38-11.8590.054319702190.05100
11.85-29.577.90.0638.39921250.0694.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.65→29.566 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 12.332 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.214
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY (4). UNEXPLAINED ELECTRON DENSITIES NEAR RESIDUE 6 IN B CHAIN WERE NOT MODELED. (5). THIOCYANATE (SCN) IONS FROM CRYO SOLUTION WERE MODELED. (6). THE RESIDUES 66-95 IN A AND B CHAINS WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS AND THEY WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 427 4.7 %RANDOM
Rwork0.188 ---
obs0.19 9041 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.85 Å2 / Biso mean: 26.137 Å2 / Biso min: 10.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20.74 Å20 Å2
2--1.48 Å20 Å2
3----2.22 Å2
Refinement stepCycle: LAST / Resolution: 2.65→29.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 6 58 1039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211038
X-RAY DIFFRACTIONr_bond_other_d0.0010.02685
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.8911416
X-RAY DIFFRACTIONr_angle_other_deg0.87331656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39321.77845
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53515157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.029159
X-RAY DIFFRACTIONr_chiral_restr0.0790.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021166
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02225
X-RAY DIFFRACTIONr_nbd_refined0.2650.2188
X-RAY DIFFRACTIONr_nbd_other0.1920.2634
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2482
X-RAY DIFFRACTIONr_nbtor_other0.0840.2560
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.241
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.29
X-RAY DIFFRACTIONr_mcbond_it1.4713645
X-RAY DIFFRACTIONr_mcbond_other0.2923254
X-RAY DIFFRACTIONr_mcangle_it2.42351039
X-RAY DIFFRACTIONr_scbond_it1.6483393
X-RAY DIFFRACTIONr_scangle_it2.4585377
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1188MEDIUM POSITIONAL0.140.5
1232LOOSE POSITIONAL0.285
1188MEDIUM THERMAL0.682
1232LOOSE THERMAL1.8410
2338LOOSE POSITIONAL0.635
2338LOOSE THERMAL3.5210
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 30 -
Rwork0.278 615 -
all-645 -
obs--100 %
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)
12.50221.51560.4344.21260.74824.81360.0591-0.0949-0.31960.02670.0382-0.07090.6957-0.0268-0.09730.11450.05510.0079-0.0706-0.0210.007336.57695.85268.4584
25.41741.87911.5253.84071.6614.85040.117-0.2263-0.1190.1362-0.0257-0.41880.1940.4909-0.09130.02320.0492-0.00890.010.0356-0.051445.888815.96719.8054
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 65
2X-RAY DIFFRACTION2B4 - 65

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