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- PDB-1ic0: RED COPPER PROTEIN NITROSOCYANIN FROM NITROSOMONAS EUROPAEA -

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Basic information

Entry
Database: PDB / ID: 1ic0
TitleRED COPPER PROTEIN NITROSOCYANIN FROM NITROSOMONAS EUROPAEA
ComponentsNitrosocyanin
KeywordsMETAL BINDING PROTEIN / red copper / cupredoxin / beta hairpin / nitrosocyanin / Nitrosomonas europaea / Cu-MAD
Function / homology
Function and homology information


Nitrosocyanin / EfeO-type cupredoxin-like domain / Cupredoxin-like domain / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Chain A, Red Copper Protein Nitrosocyanin
Similarity search - Component
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsLieberman, R.L. / Arciero, D.M. / Hooper, A.B. / Rosenzweig, A.C.
CitationJournal: Biochemistry / Year: 2001
Title: Crystal structure of a novel red copper protein from Nitrosomonas europaea.
Authors: Lieberman, R.L. / Arciero, D.M. / Hooper, A.B. / Rosenzweig, A.C.
History
DepositionMar 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrosocyanin
B: Nitrosocyanin
C: Nitrosocyanin
D: Nitrosocyanin
E: Nitrosocyanin
F: Nitrosocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,77312
Polymers73,3916
Non-polymers3816
Water4,468248
1
A: Nitrosocyanin
B: Nitrosocyanin
C: Nitrosocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8866
Polymers36,6963
Non-polymers1913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-30 kcal/mol
Surface area14300 Å2
MethodPISA
2
D: Nitrosocyanin
E: Nitrosocyanin
F: Nitrosocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8866
Polymers36,6963
Non-polymers1913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-31 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.903, 92.708, 97.201
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Nitrosocyanin


Mass: 12231.875 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Nitrosomonas europaea (bacteria) / References: UniProt: Q820S6
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Hepes, Citrate, Jeffamine M-600, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 23K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
21.4 Mtrisodium citrate1reservoir
30.1 MHEPES1reservoir
45 %(v/v)Jaffamine M-6001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.41097,1.38035,1.37957,1.3495
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 22, 1999
RadiationMonochromator: Si(111) double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.410971
21.380351
31.379571
41.34951
ReflectionResolution: 2.1→30 Å / Num. all: 570947 / Num. obs: 41643 / % possible obs: 98.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 13.7 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.055
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4 % / Rmerge(I) obs: 0.18 / % possible all: 0.98
Reflection
*PLUS
Lowest resolution: 500 Å / Num. measured all: 570947 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.18

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.26 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 564210.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 8539 9.8 %RANDOM
Rwork0.215 ---
all0.215 92597 --
obs0.215 87277 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.92 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 41 Å2
Baniso -1Baniso -2Baniso -3
1-5.3 Å20 Å20 Å2
2---3.2 Å20 Å2
3----2.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5104 0 6 248 5358
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d28.3
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it3.591.5
X-RAY DIFFRACTIONc_mcangle_it5.752
X-RAY DIFFRACTIONc_scbond_it5.842
X-RAY DIFFRACTIONc_scangle_it8.262.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 1362 9.9 %
Rwork0.26 12340 -
obs--88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.305 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.26

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