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- PDB-2vov: An oxidized tryptophan facilitates copper-binding in Methylococcu... -

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Basic information

Entry
Database: PDB / ID: 2vov
TitleAn oxidized tryptophan facilitates copper-binding in Methylococcus capsulatus secreted protein MopE. The structure of wild-type MopE to 1.35AA
ComponentsSURFACE-ASSOCIATED PROTEIN
KeywordsMETAL BINDING PROTEIN / METAL-BINDING PROTEIN / OXIDIZED TRYPTOPHAN / METHANOTROPH BACTERIUM / KUNURENINE / COPPER HOMEOSTASIS
Function / homology
Function and homology information


outer membrane / extracellular region / metal ion binding
Similarity search - Function
Putative metal-binding motif / Putative metal-binding motif / Jelly Rolls - #1220 / Copper(I)-binding protein CorA / Copper(I)-binding protein CorA-like / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Surface-associated protein / Surface-associated protein
Similarity search - Component
Biological speciesMETHYLOCOCCUS CAPSULATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHelland, R. / Fjellbirkeland, A. / Karlsen, O.A. / Ve, T. / Lillehaug, J.R. / Jensen, H.B.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: An Oxidized Tryptophan Facilitates Copper Binding in Methylococcus Capsulatus-Secreted Protein Mope.
Authors: Helland, R. / Fjellbirkeland, A. / Karlsen, O.A. / Ve, T. / Lillehaug, J.R. / Jensen, H.B.
History
DepositionFeb 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SURFACE-ASSOCIATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2893
Polymers36,1861
Non-polymers1042
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.990, 88.570, 101.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2200-

HOH

21A-2385-

HOH

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Components

#1: Protein SURFACE-ASSOCIATED PROTEIN / MOPE


Mass: 36185.836 Da / Num. of mol.: 1 / Fragment: RESIDUES 205-540 / Source method: isolated from a natural source / Details: UNIVERSITY OF WARWICK CULTURE COLLECTION / Source: (natural) METHYLOCOCCUS CAPSULATUS (bacteria) / Strain: BATH, NCIMB 11132 / References: UniProt: Q9AIP9, UniProt: G1UBC6*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsKYNURENINE (KYN): TRYPTOPHAN 130 IS POST-TRANSLATIONALLY OXIDIZED TO KYNURENINE
Sequence detailsTHE PURIFIED MOPE REPRESENTS THE 336 C-TERMINAL RESIDUES OF THE SEQUENCE. THE 46 N-TERMINAL ...THE PURIFIED MOPE REPRESENTS THE 336 C-TERMINAL RESIDUES OF THE SEQUENCE. THE 46 N-TERMINAL RESIDUES OF THE PURIFIED MOPE IS NOT VISIBLE IN ELECTRON DENSITY.

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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: 2.2 Å3/Da / Density % sol: 43.68 % / Description: NONE
Crystal growpH: 7.5 / Details: 36-45% AMMONIUM SULFATE, 0.1 M HEPES PH 7.25-7.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8722
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8722 Å / Relative weight: 1
ReflectionResolution: 1.35→28.3 Å / Num. obs: 71009 / % possible obs: 98.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 8.6
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 1.6 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.3.0021refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VOX

2vox


Resolution: 1.35→28.3 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.207 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TRYPTOPHAN 130 IS POST-TRANSLATIONALLY MODIFIED TO KYNURENINE RESIDUES 1-46 ARE NOT VISIBLE IN ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.211 3583 5 %RANDOM
Rwork0.193 ---
obs0.194 67423 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.35→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2234 0 2 390 2626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222345
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.9533218
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7724.83993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.55315342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.687154
X-RAY DIFFRACTIONr_chiral_restr0.0710.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021836
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.31099
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.51625
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.5568
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.329
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.539
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5271.51503
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.96922392
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it12.1813994
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.8314.5826
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
LS refinement shellResolution: 1.35→1.39 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.314 222
Rwork0.312 4892

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