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- PDB-5zl1: Hexameric structure of copper-containing nitrite reductase of an ... -

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Basic information

Entry
Database: PDB / ID: 5zl1
TitleHexameric structure of copper-containing nitrite reductase of an anammox organism KSU-1
ComponentsPutative copper-type nitrite reductase
KeywordsOXIDOREDUCTASE / Copper-containing nitrite reductase
Function / homology
Function and homology information


nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / copper ion binding
Similarity search - Function
Nitrite reductase, copper-type / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesCandidatus Jettenia caeni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHira, D. / Matsumura, M. / Kitamura, R. / Fujii, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJSPS KAKENHI 16K07703 Japan
CitationJournal: To Be Published
Title: Hexameric structure of copper-containing nitrite reductase of an anammox organism KSU-1
Authors: Hira, D. / Matsumura, M. / Kitamura, R. / Fujii, T.
History
DepositionMar 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_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_conn.ptnr2_symmetry / _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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative copper-type nitrite reductase
B: Putative copper-type nitrite reductase
C: Putative copper-type nitrite reductase
D: Putative copper-type nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,02321
Polymers143,9074
Non-polymers1,11617
Water61334
1
A: Putative copper-type nitrite reductase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)217,44030
Polymers215,8606
Non-polymers1,57924
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area20920 Å2
ΔGint-354 kcal/mol
Surface area57990 Å2
MethodPISA
2
B: Putative copper-type nitrite reductase
C: Putative copper-type nitrite reductase
D: Putative copper-type nitrite reductase
hetero molecules

B: Putative copper-type nitrite reductase
C: Putative copper-type nitrite reductase
D: Putative copper-type nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,56732
Polymers215,8606
Non-polymers1,70626
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area21730 Å2
ΔGint-373 kcal/mol
Surface area58060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)270.217, 270.217, 128.909
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 21 - 326 / Label seq-ID: 21 - 326

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Putative copper-type nitrite reductase


Mass: 35976.699 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Jettenia caeni (bacteria) / Gene: KSU1_D0929 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: I3IR93
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100mM Tris-HCl, 500mM lithium sulfate, 4% PEG 4000 (pH8.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 29860 / % possible obs: 100 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.038 / Rrim(I) all: 0.13 / Χ2: 1.255 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
3.2-3.2611.50.56914820.9330.1760.5961.102
3.26-3.3111.50.47214940.9580.1450.4941.075
3.31-3.3811.60.45314810.9520.1390.4741.103
3.38-3.4511.60.35114790.9740.1080.3671.106
3.45-3.5211.60.30714840.9820.0940.3211.104
3.52-3.611.60.25714710.9870.0790.2691.117
3.6-3.6911.60.21814850.9890.0670.2281.136
3.69-3.7911.60.21314840.990.0650.2231.138
3.79-3.9111.60.17914730.9930.0550.1881.129
3.91-4.0311.60.1514920.9950.0460.1571.168
4.03-4.1811.60.12414760.9970.0380.1291.217
4.18-4.3411.60.10115000.9970.0310.1061.23
4.34-4.5411.60.0914790.9980.0280.0941.258
4.54-4.7811.60.07715100.9980.0240.081.242
4.78-5.0811.60.07414890.9980.0230.0771.319
5.08-5.4711.50.08614850.9980.0260.091.511
5.47-6.0211.50.09115120.9970.0280.0951.709
6.02-6.8911.50.08315050.9980.0250.0861.678
6.89-8.6711.40.05815140.9990.0180.061.335
8.67-50110.0415650.9990.0130.0421.415

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KBW

1kbw


Resolution: 3.2→40 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.868 / SU B: 22.064 / SU ML: 0.375 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.482
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 1507 5.1 %RANDOM
Rwork0.2403 ---
obs0.241 28237 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 121.2 Å2 / Biso mean: 55.878 Å2 / Biso min: 11.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å2-0.7 Å20 Å2
2---1.39 Å20 Å2
3---4.52 Å2
Refinement stepCycle: final / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9548 0 33 34 9615
Biso mean--71.73 28.89 -
Num. residues----1224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199893
X-RAY DIFFRACTIONr_bond_other_d0.0090.029176
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.94313360
X-RAY DIFFRACTIONr_angle_other_deg1.525321152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1351220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.223.947456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.749151524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2251544
X-RAY DIFFRACTIONr_chiral_restr0.0780.21408
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02111188
X-RAY DIFFRACTIONr_gen_planes_other0.010.022304
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A375820.07
12B375820.07
21A368360.1
22C368360.1
31A368940.09
32D368940.09
41B368620.1
42C368620.1
51B370040.08
52D370040.08
61C369340.1
62D369340.1
LS refinement shellResolution: 3.2→3.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 92 -
Rwork0.316 2084 -
all-2176 -
obs--100 %

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