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Basic information

Entry
Database: PDB / ID: 5xzj
TitleCrystal structure of the Zn-directed tetramer of the engineered cyt cb562 variant, C96T/AB5
ComponentsSoluble cytochrome b562
KeywordsELECTRON TRANSPORT / de novo protein
Function / homology
Function and homology information


electron transport chain / electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
HEME C / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.98 Å
AuthorsSong, W.J. / Tezcan, F.A.
Funding support Korea, Republic Of, United States, 2items
OrganizationGrant numberCountry
NRF2016R1C1B2007898 Korea, Republic Of
National Science Foundation (NSF, United States)CHE1306646 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Importance of Scaffold Flexibility/Rigidity in the Design and Directed Evolution of Artificial Metallo-beta-lactamases.
Authors: Song, W.J. / Yu, J. / Tezcan, F.A.
History
DepositionJul 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 2.0Oct 2, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id
Revision 2.2Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_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

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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)50,70623
Polymers47,2814
Non-polymers3,42519
Water5,188288
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.747, 63.481, 127.785
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21C
12C
22B
13B
23A

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 6 / Auth seq-ID: 1 - 106 / Label seq-ID: 1 - 106

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11DD
21CC
12CC
22BB
13BB
23AA

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.163235, -0.075537, -0.983691), (-0.080958, -0.992677, 0.089661), (-0.98326, 0.094273, 0.155924)2.81029, 10.17517, 1.61548
3given(1), (1), (1)
4given(-0.014589, 0.565827, 0.824395), (0.59227, -0.65939, 0.463056), (0.805608, 0.49502, -0.325502)26.51107, 4.56712, -34.405102
5given(1), (1), (1)
6given(-0.154975, -0.073684, -0.985167), (-0.040503, -0.995902, 0.080859), (-0.987088, 0.052434, 0.151356)2.55908, 9.33315, 1.40697

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Components

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


Mass: 11820.182 Da / Num. of mol.: 4
Mutation: R34A, L38A, Q41W, K42S, K59H, D66W, V69I, D73H, K77H, E86D, A89E, Q93H, R98C, A100H, 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-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 45% 2-methyl-2,4-pentanediol 400, 0.1M HEPES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→63.893 Å / Num. all: 35176 / Num. obs: 35176 / % possible obs: 99.9 % / Redundancy: 5.8 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.064 / Rsym value: 0.059 / Net I/av σ(I): 10.6 / Net I/σ(I): 17.8 / Num. measured all: 203462
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.98-2.0960.511.40.2260.5590.51100
2.09-2.215.90.322.40.1420.3510.32100
2.21-2.375.60.2073.80.0950.2280.20799.8
2.37-2.565.90.1445.40.0640.1580.144100
2.56-2.860.0967.90.0430.1060.09699.9
2.8-3.135.60.06311.70.0290.070.06399.9
3.13-3.6160.04416.10.0190.0480.044100
3.61-4.435.60.03320.40.0150.0360.03399.8
4.43-6.265.50.03210.0140.0330.0399.6
6.26-35.3750.02323.80.0110.0250.02399.2

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHASERphasing
RefinementResolution: 1.98→63.89 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.105 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.148
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 1743 5 %RANDOM
Rwork0.1768 ---
obs0.1788 33379 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 107.04 Å2 / Biso mean: 37.062 Å2 / Biso min: 18.16 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å2-0 Å2
2---0.58 Å20 Å2
3----0.42 Å2
Refinement stepCycle: final / Resolution: 1.98→63.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 187 288 3787
Biso mean--35.93 43.16 -
Num. residues----424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193588
X-RAY DIFFRACTIONr_bond_other_d0.0020.023148
X-RAY DIFFRACTIONr_angle_refined_deg1.5072.0044904
X-RAY DIFFRACTIONr_angle_other_deg1.0243.0027328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2575420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.78526.279172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76415588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.983158
X-RAY DIFFRACTIONr_chiral_restr0.1040.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024068
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02676
Refine LS restraints NCS

Dom-ID: 1 / Number: 1585 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDTypeRms dev position (Å)Weight position
1DLOOSE POSITIONAL0.365
1DLOOSE THERMAL5.3210
2CLOOSE POSITIONAL0.475
2CLOOSE THERMAL3.5410
3BLOOSE POSITIONAL0.445
3BLOOSE THERMAL2.1110
LS refinement shellResolution: 1.98→2.031 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 122 -
Rwork0.237 2434 -
all-2556 -
obs--99.96 %

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