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- PDB-3nmj: Crystal structure of a nickel mediated dimer for the phenanthroli... -

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Basic information

Entry
Database: PDB / ID: 3nmj
TitleCrystal structure of a nickel mediated dimer for the phenanthroline-modified cytochrome cb562 variant, MBP-Phen2
ComponentsSoluble cytochrome b562
KeywordsELECTRON TRANSPORT / 4-helix-bundle
Function / homology
Function and homology information


electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NICKEL (II) ION / N-1,10-phenanthrolin-5-ylacetamide / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsRadford, R.J. / Tezcan, F.A.
CitationJournal: Chem.Commun.(Camb.) / Year: 2011
Title: Porous protein frameworks with unsaturated metal centers in sterically encumbered coordination sites.
Authors: Radford, R.J. / Lawrenz, M. / Nguyen, P.C. / McCammon, J.A. / Tezcan, F.A.
History
DepositionJun 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: 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_ref_seq_dif / 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_asym_id / _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_asym_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_asym_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.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_ref_seq_dif.details / _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: Soluble cytochrome b562
B: Soluble cytochrome b562
C: Soluble cytochrome b562
D: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,38014
Polymers45,8484
Non-polymers3,53210
Water724
1
A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3163
Polymers11,4621
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3744
Polymers11,4621
Non-polymers9123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3744
Polymers11,4621
Non-polymers9123
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3163
Polymers11,4621
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.291, 99.291, 109.317
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 106
2111B1 - 106
3111C1 - 106
4111D1 - 106

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Components

#1: Protein
Soluble cytochrome b562 / Cytochrome b-562


Mass: 11461.927 Da / Num. of mol.: 4 / Mutation: W59C, R62A, H63A, D66A, R98C, Y101C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-PXX / N-1,10-phenanthrolin-5-ylacetamide


Mass: 237.257 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H11N3O
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.39 Å3/Da / Density % sol: 63.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 400, 0.1 M Tris, 0.2 ammonium sulfate, 6.2 mM nickel sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2009
RadiationMonochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→85.99 Å / Num. all: 11200 / Num. obs: 11200 / % possible obs: 100 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 1.4 / Redundancy: 9.9 % / Rsym value: 0.178 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.1-3.279.80.4331.41585016100.433100
3.27-3.479.80.3591.61521615480.359100
3.47-3.719.80.2841.91427314500.284100
3.71-4100.2382.31353213590.238100
4-4.38100.2172.41230412260.217100
4.38-4.910.10.1782.61142911320.178100
4.9-5.6610.10.1583.1100529960.158100
5.66-6.93100.1253.884148380.125100
6.93-9.89.80.065864936650.065100
9.8-85.9899.30.0528.835083760.05299.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.81 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.1 Å85.99 Å
Translation3.1 Å85.99 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→85.99 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.2737 / WRfactor Rwork: 0.2364 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.833 / SU B: 16.666 / SU ML: 0.298 / SU Rfree: 0.435 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.435 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 776 6.9 %RANDOM
Rwork0.1932 ---
all0.1963 11170 --
obs0.1963 11169 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 86.1 Å2 / Biso mean: 53.6081 Å2 / Biso min: 14.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 3.1→85.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3187 0 246 4 3437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223531
X-RAY DIFFRACTIONr_angle_refined_deg0.7422.1634777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5695419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.95927.838148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.7715608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.389158
X-RAY DIFFRACTIONr_chiral_restr0.0550.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212660
X-RAY DIFFRACTIONr_mcbond_it0.981.52119
X-RAY DIFFRACTIONr_mcangle_it2.03423361
X-RAY DIFFRACTIONr_scbond_it3.51731404
X-RAY DIFFRACTIONr_scangle_it5.8014.51416
Refine LS restraints NCS

Ens-ID: 1 / Number: 793 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.10.05
2BTIGHT POSITIONAL0.10.05
3CTIGHT POSITIONAL0.10.05
4DTIGHT POSITIONAL0.10.05
1ATIGHT THERMAL0.250.5
2BTIGHT THERMAL0.240.5
3CTIGHT THERMAL0.250.5
4DTIGHT THERMAL0.250.5
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 49 -
Rwork0.244 770 -
all-819 -
obs--100 %

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