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- PDB-4bz4: CorA is a surface-associated copper-binding protein important in ... -

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Basic information

Entry
Database: PDB / ID: 4bz4
TitleCorA is a surface-associated copper-binding protein important in Methylomicrobium album BG8 copper acquisition
ComponentsCOPPER-REPRESSIBLE POLYPEPTIDE
KeywordsCOPPER-BINDING PROTEIN / COPPER ACQUISITION / METHANOTROPH
Function / homology
Function and homology information


Jelly Rolls - #1220 / Copper(I)-binding protein CorA / Copper(I)-binding protein CorA-like / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (I) ION / Copper(I)-binding protein CorA domain-containing protein / Copper-repressible polypeptide
Similarity search - Component
Biological speciesMETHYLOMICROBIUM ALBUM BG8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 Å
AuthorsJohnson, K.A. / Ve, T. / Pedersen, R.B. / Lillehaug, J.R. / Jensen, H.B. / Helland, R. / Karlsen, O.A.
CitationJournal: Plos One / Year: 2014
Title: Cora is a Copper Repressible Surface-Associated Copper(I)-Binding Protein Produced in Methylomicrobium Album Bg8.
Authors: Johnson, K.A. / Ve, T. / Larsen, O. / Pedersen, R.B. / Lillehaug, J.R. / Jensen, H.B. / Helland, R. / Karlsen, O.A.
History
DepositionJul 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COPPER-REPRESSIBLE POLYPEPTIDE
B: COPPER-REPRESSIBLE POLYPEPTIDE
C: COPPER-REPRESSIBLE POLYPEPTIDE
D: COPPER-REPRESSIBLE POLYPEPTIDE
E: COPPER-REPRESSIBLE POLYPEPTIDE
F: COPPER-REPRESSIBLE POLYPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,36835
Polymers150,4756
Non-polymers4,89329
Water21,1681175
1
A: COPPER-REPRESSIBLE POLYPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9426
Polymers25,0791
Non-polymers8635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: COPPER-REPRESSIBLE POLYPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9426
Polymers25,0791
Non-polymers8635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: COPPER-REPRESSIBLE POLYPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9426
Polymers25,0791
Non-polymers8635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: COPPER-REPRESSIBLE POLYPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6595
Polymers25,0791
Non-polymers5804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: COPPER-REPRESSIBLE POLYPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2247
Polymers25,0791
Non-polymers1,1456
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: COPPER-REPRESSIBLE POLYPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6595
Polymers25,0791
Non-polymers5804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.840, 113.170, 81.490
Angle α, β, γ (deg.)90.00, 104.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
COPPER-REPRESSIBLE POLYPEPTIDE / CORA


Mass: 25079.221 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: MODIFICATION OF RESIDUE 62. TRYPTOPHAN IS OXIDIZED TO KYNURENINE
Source: (natural) METHYLOMICROBIUM ALBUM BG8 (bacteria) / References: UniProt: P71489, UniProt: H8GPE3*PLUS

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Non-polymers , 5 types, 1204 molecules

#2: Chemical
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1175 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE FIRST RESIDUE VISIBLE IN ELECTRON DENSITY IS NUMBER 28 IN THE SEQUENCE. OTHER RESIDUES NOT ...THE FIRST RESIDUE VISIBLE IN ELECTRON DENSITY IS NUMBER 28 IN THE SEQUENCE. OTHER RESIDUES NOT INCLUDED IN THE STRUCTURE ARE DUE TO LACK OF WELL DEFINED 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: 2.11 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 7 / Details: 11.5-14% PEG 8K, 0.1 BISTRIS PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9794, 1.5418
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
21.54181
ReflectionResolution: 1.6→30 Å / Num. obs: 168264 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.3
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.8 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
SOLVEphasing
RESOLVEphasing
MOLREPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.479 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS ARE NOT INCLUDED IN THE STRUCTURE. THE ORIENTATIONS OF MET57 ARE ONLY MODELED, AND GIVEN ZERO OCCUPANCY, DUE TO UNUSUAL ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS ARE NOT INCLUDED IN THE STRUCTURE. THE ORIENTATIONS OF MET57 ARE ONLY MODELED, AND GIVEN ZERO OCCUPANCY, DUE TO UNUSUAL ELECTRON DENSITY SURROUNDING THE MAIN CHAIN AND SIDE CHAIN OF THIS AND THE FOLLOWING RESIDUE.
RfactorNum. reflection% reflectionSelection details
Rfree0.18809 8427 5 %RANDOM
Rwork0.15753 ---
obs0.15906 159775 98.72 %-
Solvent computationIon probe radii: 0 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.349 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å2-0.35 Å2
2--0.35 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9194 0 173 1175 10542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0199707
X-RAY DIFFRACTIONr_bond_other_d0.0010.028899
X-RAY DIFFRACTIONr_angle_refined_deg2.011.95213179
X-RAY DIFFRACTIONr_angle_other_deg0.8973.00220502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73751192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44424.494405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.169151392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9361524
X-RAY DIFFRACTIONr_chiral_restr0.1260.21397
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02110988
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022202
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
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 646 -
Rwork0.239 11774 -
obs--98.75 %

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