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- PDB-3qvy: Crystal structure of the Zn-RIDC1 complex stabilized by BMOE cros... -

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Basic information

Entry
Database: PDB / ID: 3qvy
TitleCrystal structure of the Zn-RIDC1 complex stabilized by BMOE crosslinks
ComponentsCytochrome cb562
KeywordsOXIDOREDUCTASE / Four-helix bundle
Function / homologyCytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / PROTOPORPHYRIN IX CONTAINING FE / 1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSalgado, E.N. / Tezcan, F.A.
CitationJournal: Inorg.Chem. / Year: 2011
Title: Templated construction of a zn-selective protein dimerization motif.
Authors: Salgado, E.N. / Brodin, J.D. / To, M.M. / Tezcan, F.A.
History
DepositionFeb 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome cb562
B: Cytochrome cb562
C: Cytochrome cb562
D: Cytochrome cb562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,73723
Polymers46,9814
Non-polymers3,75719
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint-324 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.088, 52.088, 253.943
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
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
Cytochrome cb562


Mass: 11745.175 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ME7 / 1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione)


Mass: 220.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8N2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, 10% PEG 3350, 4.6 mM zinc chloride, pH 7.5, 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: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 10, 2010
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
111.000H, 1.000K, L10.504
11-1.000H-1.000K, 1.000K, -L20.496
ReflectionResolution: 2.3→253.943 Å / Num. all: 17118 / Num. obs: 17118 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.1 % / Rsym value: 0.052 / Net I/σ(I): 31.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.42110.2483.12750624940.24899.1
2.42-2.57110.1784.32605723600.17899.2
2.57-2.7511.10.1395.42477322400.13999.2
2.75-2.9711.10.0898.32250620310.08999.4
2.97-3.2511.10.06810.72149819410.06899.5
3.25-3.6411.10.04913.51895217080.04999.5
3.64-4.211.10.03816.41688115230.03899.7
4.2-5.1411.10.03217.71428112900.03299.8
5.14-7.27110.0317.91110010060.0399.6
7.27-42.50710.80.03117.856905250.03195.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→42.51 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.498 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2862 1258 7.3 %RANDOM
Rwork0.242 ---
obs0.2453 17117 99.16 %-
all-17262 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.02 Å2 / Biso mean: 36.418 Å2 / Biso min: 11.82 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å20 Å2
2--1.44 Å20 Å2
3----2.88 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 217 23 3524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0233632
X-RAY DIFFRACTIONr_angle_refined_deg1.8052.1064912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5895420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.71126.585164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.41215588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.329158
X-RAY DIFFRACTIONr_chiral_restr0.1120.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212760
X-RAY DIFFRACTIONr_mcbond_it0.6631.52132
X-RAY DIFFRACTIONr_mcangle_it1.31523384
X-RAY DIFFRACTIONr_scbond_it2.49331500
X-RAY DIFFRACTIONr_scangle_it3.6394.51528
Refine LS restraints NCS

Ens-ID: 1 / Number: 821 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.080.05
2BTIGHT POSITIONAL0.070.05
3CTIGHT POSITIONAL0.110.05
4DTIGHT POSITIONAL0.070.05
1ATIGHT THERMAL0.160.5
2BTIGHT THERMAL0.150.5
3CTIGHT THERMAL0.160.5
4DTIGHT THERMAL0.150.5
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 106 -
Rwork0.319 1142 -
all-1248 -
obs--97.42 %

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