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- PDB-9msz: 1.1 A Crystal Structure of Housefly Cytochrome c at pH 9.7 -

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Basic information

Entry
Database: PDB / ID: 9msz
Title1.1 A Crystal Structure of Housefly Cytochrome c at pH 9.7
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
BICARBONATE ION / HEME C / Cytochrome c
Similarity search - Component
Biological speciesMusca domestica (house fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,6155
Polymers23,3172
Non-polymers1,2983
Water6,630368
1
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3383
Polymers11,6581
Non-polymers6802
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)34.038, 59.682, 52.127
Angle α, β, γ (deg.)90.000, 106.865, 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: Wing 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-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 281 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

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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: 1.1→32.575 Å / Num. obs: 76813 / % possible obs: 95.04 % / Observed criterion σ(I): -3 / Redundancy: 12.16 % / Biso Wilson estimate: 9.22 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.023 / Rrim(I) all: 0.076 / Net I/σ(I): 19.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) all% possible all
1.1-1.135.890.2255.639920.9630.990.1060.27864.29
1.13-1.167.270.2067.851160.9790.9950.0780.22182.76
1.16-1.29.660.18310.358950.9880.9970.0610.19395.73
1.2-1.2413.10.16713.161110.9920.9980.0490.17498.52
1.24-1.2913.440.1481561690.9930.9980.0420.15499.13
1.29-1.3513.580.12517.461340.9950.9990.0350.1399.26
1.35-1.4213.660.10819.461860.9960.9990.0310.1399.47
1.42-1.5113.740.0922.361640.9970.9990.0250.09399.74
1.51-1.6313.810.07824.562360.9980.9990.0220.08199.89
1.63-1.7913.920.0726.862290.99810.0190.072100
1.79-2.0513.910.0642962090.99810.0180.066100
2.05-2.5913.490.06230.562590.9980.9990.0180.064100
2.59-32.57510.140.06626.261140.9910.9980.0250.07196.62

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Processing

Software
NameVersionClassification
PHENIXdev_3150refinement
PHENIXdev_3150refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→32.575 Å / SU ML: 0.0632 / Cross valid method: FREE R-VALUE / σ(F): 0.55 / Phase error: 13.9739 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1509 1869 2.43 %
Rwork0.1307 74935 -
obs0.1312 76804 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.39 Å2
Refinement stepCycle: LAST / Resolution: 1.1→32.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 90 368 2100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091877
X-RAY DIFFRACTIONf_angle_d1.15622559
X-RAY DIFFRACTIONf_chiral_restr0.0782247
X-RAY DIFFRACTIONf_plane_restr0.0124327
X-RAY DIFFRACTIONf_dihedral_angle_d13.939689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.130.1795960.17773892X-RAY DIFFRACTION64.21
1.13-1.160.1571180.13055000X-RAY DIFFRACTION82.78
1.16-1.20.15271480.11765750X-RAY DIFFRACTION95.72
1.2-1.240.13621490.11685959X-RAY DIFFRACTION98.52
1.24-1.290.17491530.11926011X-RAY DIFFRACTION99.12
1.29-1.350.14881430.11465993X-RAY DIFFRACTION99.27
1.35-1.420.13251540.10736029X-RAY DIFFRACTION99.45
1.42-1.510.11311460.10376018X-RAY DIFFRACTION99.74
1.51-1.630.13421520.10816084X-RAY DIFFRACTION99.89
1.63-1.790.15911480.11926082X-RAY DIFFRACTION99.98
1.79-2.050.16731550.13426052X-RAY DIFFRACTION100
2.05-2.590.15741550.13676105X-RAY DIFFRACTION100
2.59-32.5750.15031520.15035960X-RAY DIFFRACTION96.62

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