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- PDB-5xzi: Crystal structure of the Zn-directed tetramer of the engineered c... -

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Basic information

Entry
Database: PDB / ID: 5xzi
TitleCrystal structure of the Zn-directed tetramer of the engineered cyt cb562 variant, AB5
ComponentsSoluble cytochrome b562
KeywordsELECTRON TRANSPORT / de novo protein
Function / homologyCytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / electron transfer activity / periplasmic space / iron ion binding / heme binding / HEME C / Soluble cytochrome b562
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.65 Å
AuthorsSong, W.J. / Tezcan, F.A.
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: Atomic model / Data collection ...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 / 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 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6787
Polymers11,8221
Non-polymers8566
Water1,18966
1
A: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,71228
Polymers47,2894
Non-polymers3,42324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544x,-y-1/2,-z-1/21
crystal symmetry operation11_454-x-1/2,y,-z-1/21
crystal symmetry operation14_445-x-1/2,-y-1/2,z1
Buried area10070 Å2
ΔGint-499 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.290, 98.000, 99.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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Components

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


Mass: 11822.221 Da / Num. of mol.: 1
Mutation: R34A, L38A, Q41W, K42S, K59H, D66W, V69I, D73H, K77H, E86D, A89E, Q93H, T96C, 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 / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 31.5% 2-methyl-2,4-pentanediol 400, 0.1M HEPES, pH 7.5, 0.2M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.65→49.665 Å / Num. all: 3383 / Num. obs: 3383 / % possible obs: 91.5 % / Redundancy: 3.8 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.045 / Rsym value: 0.039 / Net I/av σ(I): 9.7 / Net I/σ(I): 25.6 / Num. measured all: 12901
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.65-2.793.80.05511.10.0320.0640.05582.4
2.79-2.963.70.0511.90.030.0590.0598
2.96-3.173.60.04413.30.0250.0510.04495.4
3.17-3.424.20.03716.60.0210.0420.03799.2
3.42-3.754.10.03219.80.0170.0370.03277.1
3.75-4.193.80.03120.30.0170.0360.03189.1
4.19-4.843.50.03119.50.0180.0370.03193.1
4.84-5.934.10.032200.0170.0360.03298.2
5.93-8.383.70.03711.90.0220.0440.03794.6
8.38-26.4093.70.0668.90.0380.0770.06692.1

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementResolution: 2.65→49.665 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.892 / SU B: 14.287 / SU ML: 0.292 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.396
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 170 5 %RANDOM
Rwork0.1902 ---
obs0.1944 3213 90.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.38 Å2 / Biso mean: 55.317 Å2 / Biso min: 12.46 Å2
Baniso -1Baniso -2Baniso -3
1-3.7 Å2-0 Å2-0 Å2
2---0.61 Å2-0 Å2
3----3.09 Å2
Refinement stepCycle: final / Resolution: 2.65→49.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 48 66 941
Biso mean--57.44 42.06 -
Num. residues----106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.019896
X-RAY DIFFRACTIONr_bond_other_d0.0020.02785
X-RAY DIFFRACTIONr_angle_refined_deg1.6592.0041224
X-RAY DIFFRACTIONr_angle_other_deg1.0613.0021828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5275105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.46326.27943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.30615147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.143152
X-RAY DIFFRACTIONr_chiral_restr0.090.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021017
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02169
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 7 -
Rwork0.091 159 -
all-166 -
obs--64.59 %

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