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- PDB-4b2n: Latex Oxygenase RoxA -

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Basic information

Entry
Database: PDB / ID: 4b2n
TitleLatex Oxygenase RoxA
Components70 KDA PROTEIN
KeywordsELECTRON TRANSPORT / CYTOCHROME / RUBBER OXYGENASE / DIOXYGENASE
Function / homology
Function and homology information


cytochrome-c peroxidase activity / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
RoxA-like, cytochrome c-like / : / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / OXYGEN MOLECULE / 70 kDa protein
Similarity search - Component
Biological speciesXANTHOMONAS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsSeidel, J. / Schmitt, G. / Hoffmann, M. / Jendrossek, D. / Einsle, O.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2013
Title: Structure of the processive rubber oxygenase RoxA from Xanthomonas sp.
Authors: Seidel, J. / Schmitt, G. / Hoffmann, M. / Jendrossek, D. / Einsle, O.
History
DepositionJul 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Atomic model
Revision 1.2Aug 14, 2013Group: Database references
Revision 1.3Sep 4, 2013Group: Database references
Revision 1.4Oct 9, 2013Group: Other
Revision 2.0Jan 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / refine / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_validate_close_contact.auth_comp_id_2 / _refine.pdbx_starting_model / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Jul 10, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 70 KDA PROTEIN
B: 70 KDA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,89610
Polymers145,8822
Non-polymers3,0158
Water31,7421762
1
A: 70 KDA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4485
Polymers72,9411
Non-polymers1,5074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 70 KDA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4485
Polymers72,9411
Non-polymers1,5074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.368, 97.106, 101.050
Angle α, β, γ (deg.)90.00, 98.39, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 15 - 662 / Label seq-ID: 15 - 662

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 70 KDA PROTEIN / ROXA


Mass: 72940.812 Da / Num. of mol.: 2 / Fragment: RESIDUES 17-678 / Source method: isolated from a natural source / Source: (natural) XANTHOMONAS SP. (bacteria) / Strain: 35Y / References: UniProt: Q7X0P3
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1762 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.92 % / Description: NONE
Crystal growpH: 7.5 / Details: PEG 8000, HEPES/NAOH PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 126052 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.4
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKLdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→35.8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.052 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 6310 5 %RANDOM
Rwork0.16807 ---
obs0.1707 119356 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.596 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.05 Å2
2---0.05 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10116 0 206 1762 12084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0210771
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7261.97814813
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77151312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32723.264484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.033151523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8561578
X-RAY DIFFRACTIONr_chiral_restr0.1410.21503
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0228618
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 944 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 435 -
Rwork0.306 8411 -
obs--95.96 %
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)
10.1099-0.05070.07560.2079-0.0760.1523-0.0148-0.0409-0.0168-0.00570.03010.0138-0.0356-0.0186-0.01530.0140.00110.01050.0370.00340.028561.47778.53177.5174
20.2028-0.0904-0.09240.32610.16680.1263-0.0389-0.03720.01720.05960.0504-0.04110.05510.0069-0.01160.0320.0024-0.00520.0392-0.01050.013788.07051.9133-39.6548
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 701
2X-RAY DIFFRACTION2B15 - 701

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