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- PDB-5fc9: Novel Purple Cupredoxin from Nitrosopumilus maritimus -

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Basic information

Entry
Database: PDB / ID: 5fc9
TitleNovel Purple Cupredoxin from Nitrosopumilus maritimus
ComponentsBlue (Type 1) copper domain protein
KeywordsMETAL BINDING PROTEIN / Cupredoxin / NO oxidation / nitrogen cycle / open type 1 copper site
Function / homology
Function and homology information


electron transfer activity / copper ion binding
Similarity search - Function
Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Blue (Type 1) copper domain protein
Similarity search - Component
Biological speciesNitrosopumilus maritimus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHosseinzadeh, P. / Lu, Y. / Robinson, H. / Gao, Y.-G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1413328 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: A Purple Cupredoxin from Nitrosopumilus maritimus Containing a Mononuclear Type 1 Copper Center with an Open Binding Site.
Authors: Hosseinzadeh, P. / Tian, S. / Marshall, N.M. / Hemp, J. / Mullen, T. / Nilges, M.J. / Gao, Y.G. / Robinson, H. / Stahl, D.A. / Gennis, R.B. / Lu, Y.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Blue (Type 1) copper domain protein
B: Blue (Type 1) copper domain protein
C: Blue (Type 1) copper domain protein
D: Blue (Type 1) copper domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8099
Polymers42,4914
Non-polymers3185
Water10,485582
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-92 kcal/mol
Surface area15910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.887, 68.887, 184.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Blue (Type 1) copper domain protein


Mass: 10622.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Protein containing Cu ions
Source: (gene. exp.) Nitrosopumilus maritimus (strain SCM1) (archaea)
Strain: SCM1 / Gene: Nmar_1307 / Plasmid: pET22b / Details (production host): periplasmic expression / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: A9A2G4
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 582 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Crystals of N. mar_1307 were grown by the hanging drop vapor diffusion method. Protein solution was prepared in 50 mM sodium acetate buffer at pH 6.0 to a concentration of about 2 mM. A 2 uL ...Details: Crystals of N. mar_1307 were grown by the hanging drop vapor diffusion method. Protein solution was prepared in 50 mM sodium acetate buffer at pH 6.0 to a concentration of about 2 mM. A 2 uL portion of this protein solution was then mixed with 2 uL of a well buffer solution consisting of 0.1 M TrisHCl at pH 8.0, 20mM CuSO4, 0.1M LiNO3 and varying amounts of polyethylene glycol (PEG). The highest quality crystals formed from wells with 35 % w/v PEG 4000 after about 2 months at 4 C

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 59707 / % possible obs: 100 % / Redundancy: 29.5 % / Rmerge(I) obs: 0.105 / Χ2: 1.038 / Net I/av σ(I): 36.56 / Net I/σ(I): 11 / Num. measured all: 1760680
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.6-1.6628.10.71958370.879100
1.66-1.7228.30.55658580.916100
1.72-1.828.40.41158620.964100
1.8-1.928.50.29658891.044100
1.9-2.0228.60.20358971.083100
2.02-2.1728.50.14759391.069100
2.17-2.3928.50.11959471.012100
2.39-2.7428.30.10659921.08100
2.74-3.4527.70.08760801.127100
3.45-5039.20.08764061.14499.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AZU

4azu


Resolution: 1.6→45.87 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1978 3747 3.35 %
Rwork0.1731 --
obs0.174 -99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 5 582 3599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063104
X-RAY DIFFRACTIONf_angle_d1.0684264
X-RAY DIFFRACTIONf_dihedral_angle_d12.6351080
X-RAY DIFFRACTIONf_chiral_restr0.043468
X-RAY DIFFRACTIONf_plane_restr0.006564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5995-1.61980.24041400.20843934X-RAY DIFFRACTION99
1.6198-1.64110.28351390.20574027X-RAY DIFFRACTION100
1.6411-1.66360.20741370.19813958X-RAY DIFFRACTION100
1.6636-1.68730.22061410.19594048X-RAY DIFFRACTION100
1.6873-1.71250.24821360.20484004X-RAY DIFFRACTION100
1.7125-1.73930.24151450.2144022X-RAY DIFFRACTION100
1.7393-1.76780.25811430.20364041X-RAY DIFFRACTION100
1.7678-1.79830.23911400.20293952X-RAY DIFFRACTION100
1.7983-1.8310.26371420.19944016X-RAY DIFFRACTION100
1.831-1.86620.22541340.19974004X-RAY DIFFRACTION100
1.8662-1.90430.25051380.19564003X-RAY DIFFRACTION100
1.9043-1.94570.22671390.18024015X-RAY DIFFRACTION100
1.9457-1.9910.2021370.18374017X-RAY DIFFRACTION100
1.991-2.04080.20531380.18074002X-RAY DIFFRACTION100
2.0408-2.09590.19241390.17384012X-RAY DIFFRACTION100
2.0959-2.15760.17581380.17264017X-RAY DIFFRACTION100
2.1576-2.22720.18151370.1754013X-RAY DIFFRACTION100
2.2272-2.30680.18711380.16994007X-RAY DIFFRACTION100
2.3068-2.39920.23091430.17364000X-RAY DIFFRACTION100
2.3992-2.50840.20191380.18883993X-RAY DIFFRACTION100
2.5084-2.64060.22591370.19054054X-RAY DIFFRACTION100
2.6406-2.8060.21141360.18633960X-RAY DIFFRACTION100
2.806-3.02270.21161370.17584045X-RAY DIFFRACTION100
3.0227-3.32680.16631350.16993989X-RAY DIFFRACTION100
3.3268-3.8080.18091400.14894025X-RAY DIFFRACTION100
3.808-4.79680.14391400.14024005X-RAY DIFFRACTION100
4.7968-45.88920.19641400.16324005X-RAY DIFFRACTION100

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