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- PDB-4jeb: Crystal structure of an engineered RIDC1 tetramer with four inter... -

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Basic information

Entry
Database: PDB / ID: 4jeb
TitleCrystal structure of an engineered RIDC1 tetramer with four interfacial disulfide bonds and four three-coordinate Zn(II) sites
Componentssoluble cytochrome b562
KeywordsELECTRON TRANSPORT / four-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
PROTOPORPHYRIN IX CONTAINING FE / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTezcan, F.A. / Medina-Morales, A.M. / Perez, A. / Brodin, J.D.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: In Vitro and Cellular Self-Assembly of a Zn-Binding Protein Cryptand via Templated Disulfide Bonds.
Authors: Medina-Morales, A. / Perez, A. / Brodin, J.D. / Tezcan, F.A.
History
DepositionFeb 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 20, 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_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_conn.ptnr2_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5577
Polymers23,1282
Non-polymers1,4295
Water70339
1
A: soluble cytochrome b562
B: soluble cytochrome b562
hetero molecules

A: soluble cytochrome b562
B: soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,11514
Polymers46,2564
Non-polymers2,85810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554-y,-x,-z-1/31
Buried area2190 Å2
ΔGint-27 kcal/mol
Surface area24840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.942, 54.942, 145.658
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

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


Mass: 11564.073 Da / Num. of mol.: 2 / Fragment: UNP residues 23-128
Mutation: R34A, L38A, Q41W, K42S, K59A, D66W, V69I, D73H, D74A, K77H, E81C, T96C, 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) / Strain (production host): B21(DE3) / References: UniProt: P0ABE7
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 35% methyl-pentandiol, 0.1M HEPES pH 7.5, 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 30, 2012 / Details: K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.158→48.553 Å / Num. all: 13468 / Num. obs: 13468 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rsym value: 0.094 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.16-2.284.50.6921.1759717010.69284.9
2.28-2.415.70.4711.61061418710.47199.8
2.41-2.585.50.2952.6966817670.29599.6
2.58-2.795.50.193.9914016710.1999
2.79-3.055.40.1325.3846315540.13299.8
3.05-3.415.20.1065.9702713460.10697.4
3.41-3.945.10.0986.3627712380.09899.7
3.94-4.834.90.0966.5497510250.09698.2
4.83-6.834.90.0946.739978220.09497.3
6.83-36.4154.70.0659.522434730.06597.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IQ6

3iq6


Resolution: 2.3→48.55 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.207 / SU ML: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.405 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3088 812 7.1 %RANDOM
Rwork0.2436 ---
obs0.2479 11374 98.8 %-
all-13468 --
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: 89.55 Å2 / Biso mean: 57.6607 Å2 / Biso min: 26.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å21.39 Å2-0 Å2
2--2.79 Å2-0 Å2
3----4.18 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 89 39 1742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221760
X-RAY DIFFRACTIONr_angle_refined_deg1.562.0942408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1965212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.46926.49477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.70815287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.698154
X-RAY DIFFRACTIONr_chiral_restr0.1060.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211350
X-RAY DIFFRACTIONr_mcbond_it0.9161.51066
X-RAY DIFFRACTIONr_mcangle_it1.73721686
X-RAY DIFFRACTIONr_scbond_it2.4973693
X-RAY DIFFRACTIONr_scangle_it3.9774.5721
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 839 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.090.05
TIGHT THERMAL0.240.5
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 58 -
Rwork0.313 780 -
all-838 -
obs--99.76 %

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