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- PDB-9mt0: 1.2 A Crystal Structure of Housefly cytochrome c at pH 11 -

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Basic information

Entry
Database: PDB / ID: 9mt0
Title1.2 A Crystal Structure of Housefly cytochrome c at pH 11
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / metalloproteins / Insect / Protostome / cytochrome c / Alkaline pH
Function / homology
Function and homology information


mitochondrial intermembrane space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
ETHANOL / HEME C / Cytochrome c
Similarity search - Component
Biological speciesMusca domestica (house fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsZafreen, L. / Huang, L.-S. / Luemmen, P. / Berry, E.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of Insect Cytochrome c at different pH values.
Authors: Zafreen, L. / Huang, L.-S. / Luemmen, P. / Berry, E.A.
History
DepositionJan 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6005
Polymers23,3172
Non-polymers1,2833
Water5,459303
1
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3233
Polymers11,6581
Non-polymers6652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2772
Polymers11,6581
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.876, 58.634, 51.674
Angle α, β, γ (deg.)90.000, 106.772, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Cytochrome c


Mass: 11658.432 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Musca domestica (house fly) / Organ: thorax / Tissue: flight muscle / References: UniProt: A0A1I8N8V4
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.7
Details: Concentrated protein in 0.5 mM EDTA, 20 mM Tris-HCL pH 7.5 was mixed with an equal volume of precipitant containing 0.1 M Glycine pH 10.0 and 28% w/v Polyethylene Glycol Monomethyl Ether ...Details: Concentrated protein in 0.5 mM EDTA, 20 mM Tris-HCL pH 7.5 was mixed with an equal volume of precipitant containing 0.1 M Glycine pH 10.0 and 28% w/v Polyethylene Glycol Monomethyl Ether 2000 and allowed to vapor diffuse against a reservoir of the same precipitant. Before cryoprotection and freezing, the crystal was transferred to a well containing 0.1 M CAPS pH 11.0 and 28% w/v Polyethylene Glycol Monomethyl Ether 2000. The crystal fractured, and a fragment was ued for collection.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9804 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9804 Å / Relative weight: 1
ReflectionResolution: 1.2→38 Å / Num. obs: 55990 / % possible obs: 91.83 % / Observed criterion σ(I): -3 / Redundancy: 5.36 % / Biso Wilson estimate: 13.85 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.04 / Rrim(I) all: 0.097 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.2-1.242.410.4591.624780.7790.2640.53445.23
1.24-1.282.950.3982.245140.8520.2250.46181.2
1.28-1.334.260.383.153020.8980.1940.42996.33
1.33-1.45.250.3184.554060.9410.1480.35297.78
1.4-1.475.760.236.654560.9650.1040.25398.02
1.47-1.565.950.1668.954240.980.0740.18298.62
1.56-1.685.990.11911.654690.9890.0520.1399.06
1.68-1.856.140.09314.255140.9920.040.10299.26
1.85-2.126.150.07816.955360.9930.0340.08599.6
2.12-2.676.220.0761955450.9920.0330.08399.73
2.67-385.750.08118.953460.9880.0370.08994.75

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Processing

Software
NameVersionClassification
PHENIXdev_3150refinement
PHENIXdev_3150refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→37.81 Å / SU ML: 0.1264 / Cross valid method: FREE R-VALUE / σ(F): 0.93 / Phase error: 18.3377 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.165 1574 2.82 %
Rwork0.1262 54224 -
obs0.1273 55798 92.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.76 Å2
Refinement stepCycle: LAST / Resolution: 1.2→37.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 89 303 2034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861907
X-RAY DIFFRACTIONf_angle_d1.10512604
X-RAY DIFFRACTIONf_chiral_restr0.0738253
X-RAY DIFFRACTIONf_plane_restr0.0128333
X-RAY DIFFRACTIONf_dihedral_angle_d13.7568710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.240.3019700.27932581X-RAY DIFFRACTION48.48
1.24-1.280.2831190.22864450X-RAY DIFFRACTION83.67
1.28-1.330.22491590.20625120X-RAY DIFFRACTION96.26
1.33-1.40.23011480.17715220X-RAY DIFFRACTION97.69
1.4-1.470.20511480.12835230X-RAY DIFFRACTION97.87
1.47-1.560.14981510.11325198X-RAY DIFFRACTION98.54
1.56-1.680.1421610.10495304X-RAY DIFFRACTION99
1.68-1.850.15721510.1035287X-RAY DIFFRACTION99.23
1.85-2.120.16071560.1115354X-RAY DIFFRACTION99.58
2.12-2.670.15641570.11915331X-RAY DIFFRACTION99.76
2.67-37.80.15371540.12755149X-RAY DIFFRACTION94.68

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