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- PDB-3nmi: Crystal structure of the phenanthroline-modified cytochrome cb562... -

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Basic information

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


electron transport chain / periplasmic space / electron transfer activity / 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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / 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: 2.01 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_label_asym_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_label_asym_id / _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 / _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

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Assembly

Deposited unit
A: Soluble cytochrome b562
B: Soluble cytochrome b562
C: Soluble cytochrome b562
D: Soluble cytochrome b562
E: Soluble cytochrome b562
F: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,18923
Polymers68,7726
Non-polymers5,41817
Water5,134285
1
A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4345
Polymers11,4621
Non-polymers9724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 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
3
C: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3754
Polymers11,4621
Non-polymers9133
Water181
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
5
E: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4345
Polymers11,4621
Non-polymers9724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: 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)88.290, 91.787, 130.637
Angle α, β, γ (deg.)90.000, 107.990, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-188-

HOH

21B-189-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 5 / Auth seq-ID: 1 - 106 / Label seq-ID: 1 - 106

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

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


Mass: 11461.927 Da / Num. of mol.: 6 / 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


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-PXX / N-1,10-phenanthrolin-5-ylacetamide


Mass: 237.257 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H11N3O
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 3.66 Å3/Da / Density % sol: 66.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.8 M sodium acetate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 16, 2009
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.01→124.248 Å / Num. all: 65484 / Num. obs: 65484 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rsym value: 0.055 / Net I/σ(I): 17.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.01-2.124.40.2371.74217895790.23799.7
2.12-2.254.40.1442.23995890170.14499.7
2.25-2.44.40.112.43742784790.1199.5
2.4-2.594.40.0739.53514679180.07399.5
2.59-2.844.40.06210.43214772920.06299.6
2.84-3.184.40.04912.72904666530.04999.7
3.18-3.674.30.04611.32517658280.04699.7
3.67-4.494.10.03614.62025948870.03698.5
4.49-6.364.30.03317.41642738180.03398.8
6.36-43.054.10.02822821520130.02893.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.57 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.05 Å
Translation2.5 Å43.05 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→43.05 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2342 / WRfactor Rwork: 0.1965 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.838 / SU B: 3.697 / SU ML: 0.101 / SU R Cruickshank DPI: 0.1535 / SU Rfree: 0.1459 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4750 7.3 %RANDOM
Rwork0.1976 ---
all0.2003 65981 --
obs0.2003 65463 99.21 %-
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: 69.93 Å2 / Biso mean: 31.1747 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.01→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4788 0 386 285 5459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225315
X-RAY DIFFRACTIONr_angle_refined_deg0.9852.1647219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8855632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.46327.679224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.58815918
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7211514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.020.0214034
X-RAY DIFFRACTIONr_mcbond_it1.9851.53194
X-RAY DIFFRACTIONr_mcangle_it3.07425066
X-RAY DIFFRACTIONr_scbond_it4.76732121
X-RAY DIFFRACTIONr_scangle_it6.9034.52151
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A423MEDIUM POSITIONAL0.180.5
2B423MEDIUM POSITIONAL0.20.5
3C423MEDIUM POSITIONAL0.190.5
4D423MEDIUM POSITIONAL0.230.5
5E423MEDIUM POSITIONAL0.290.5
6F423MEDIUM POSITIONAL0.310.5
1A366LOOSE POSITIONAL0.555
2B366LOOSE POSITIONAL0.595
3C366LOOSE POSITIONAL0.535
4D366LOOSE POSITIONAL0.655
5E366LOOSE POSITIONAL0.695
6F366LOOSE POSITIONAL0.845
1A423MEDIUM THERMAL6.072
2B423MEDIUM THERMAL5.732
3C423MEDIUM THERMAL4.732
4D423MEDIUM THERMAL3.172
5E423MEDIUM THERMAL3.062
6F423MEDIUM THERMAL6.622
1A366LOOSE THERMAL5.8410
2B366LOOSE THERMAL5.6410
3C366LOOSE THERMAL4.4910
4D366LOOSE THERMAL3.5610
5E366LOOSE THERMAL3.8510
6F366LOOSE THERMAL5.8710
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 336 -
Rwork0.259 4493 -
all-4829 -
obs--99.61 %

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