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- PDB-9mt1: 1.53 A Crystal Structure of Housefly cytochrome c at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 9mt1
Title1.53 A Crystal Structure of Housefly cytochrome c at pH 6.5
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / metalloproteins / Insect / Protostome / cytochrome c
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 / METHANOL / Cytochrome c
Similarity search - Component
Biological speciesMusca domestica (house fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.405 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)24,7018
Polymers23,3172
Non-polymers1,3846
Water6,305350
1
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3554
Polymers11,6581
Non-polymers6973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3464
Polymers11,6581
Non-polymers6883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.222, 34.152, 105.071
Angle α, β, γ (deg.)90.000, 105.040, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-203-

NA

21A-365-

HOH

31B-455-

HOH

41B-463-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain 'A' and ((resid 8 through 10 and (name N...
221(chain 'B' and ((resid 8 through 10 and (name N...
112(chain 'A' and ((resid 43 through 49 and (name N...
222(chain 'A' and ((resid 43 through 49 and (name N...
113(chain 'A' and ((resid 57 through 59 and (name N...
223(chain 'B' and ((resid 57 through 59 and (name N...

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.482633807305, 0.872490149181, 0.0763252751637), (0.875097539901, 0.476855303523, 0.0825428080592), (0.0356216746627, 0.106630010247, -0.993660473808)-3.02428054903, -1.4855041997, 50.3481056918
2given(1), (1), (1)
3given(-0.48709477716, 0.870737981962, 0.0674836634397), (0.871220710611, 0.479063624682, 0.107109835722), (0.0609356337902, 0.110965806779, -0.991954352912)-2.73933614849, -2.34992489683, 50.6377950108

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 356 molecules

#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-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O
#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.56
Details: protein in 0.5 mM Na-EDTA, 20 mM Tris at pH of 7.5, was mixed with an equal volume of precipitant containing 0.1 M BIS-Tris pH 6.5, 28% w/v Polyethylene Glycol Monomethyl Ether 2000 and ...Details: protein in 0.5 mM Na-EDTA, 20 mM Tris at pH of 7.5, was mixed with an equal volume of precipitant containing 0.1 M BIS-Tris pH 6.5, 28% w/v Polyethylene Glycol Monomethyl Ether 2000 and allowed to equilibrate by vapor diffusion against 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: 1.405→29.196 Å / Num. obs: 36225 / % possible obs: 92.24 % / Observed criterion σ(I): -3 / Redundancy: 4.64 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.059 / Rrim(I) all: 0.138 / Net I/σ(I): 7.9
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
1.405-1.451.670.694118410.5190.8270.5810.9157.44
1.45-1.493.130.6331.628520.6770.8990.3760.74187.3
1.49-1.553.720.5232.331190.7650.9310.2930.60395.09
1.55-1.614.670.3633.731300.8910.9710.180.40896.9
1.61-1.685.090.284531520.9340.9830.1340.31596.98
1.68-1.775.080.2266.231460.9550.9880.1070.25196.59
1.77-1.885.060.1847.431380.9710.9930.0870.20496.38
1.88-2.035.110.1519.131040.9790.9950.0710.16795.48
2.03-2.235.080.12211.430850.9840.9960.0570.13594.31
2.23-2.555.080.11112.430980.9870.9970.0520.12394.28
2.55-3.225.120.10414.131650.9880.9970.0480.11595.79
3.22-29.25.390.09816.333950.9890.9970.0450.10899.47

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Processing

Software
NameVersionClassification
PHENIXdev_3150refinement
PHENIXdev_3150refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.405→29.19 Å / SU ML: 0.1453 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8901 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1853 1706 4.71 %random selection
Rwork0.1593 34513 --
obs0.1606 36219 92.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.2 Å2
Refinement stepCycle: LAST / Resolution: 1.405→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 95 350 2087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00971856
X-RAY DIFFRACTIONf_angle_d1.11042530
X-RAY DIFFRACTIONf_chiral_restr0.0782245
X-RAY DIFFRACTIONf_plane_restr0.0136323
X-RAY DIFFRACTIONf_dihedral_angle_d13.4018682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.405-1.450.3239550.33751785X-RAY DIFFRACTION57.45
1.45-1.490.3058790.26922773X-RAY DIFFRACTION87.3
1.49-1.550.27691520.22112966X-RAY DIFFRACTION95.06
1.55-1.610.23531390.18872991X-RAY DIFFRACTION96.9
1.61-1.680.17011700.1682981X-RAY DIFFRACTION96.95
1.68-1.770.1981580.15322987X-RAY DIFFRACTION96.56
1.77-1.880.20481370.15043001X-RAY DIFFRACTION96.38
1.88-2.030.19541760.15322928X-RAY DIFFRACTION95.48
2.03-2.230.16251500.13812935X-RAY DIFFRACTION94.31
2.23-2.550.17261380.14132960X-RAY DIFFRACTION94.28
2.55-3.210.16461750.14722990X-RAY DIFFRACTION95.79
3.21-29.190.17571770.15213216X-RAY DIFFRACTION99.41
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2520818099060.03396351987630.02485592371770.1046520635090.04644807392230.107846957626-0.0440670751363-0.057906993758-0.1898194484450.0882522964367-0.0518128082014-0.02189614465650.155562316074-0.00266256236901-0.0007899690610960.1181013584670.01338928070340.006542976095330.06887599554360.008407399387210.125581591105-4.79425032228-22.359467427115.6084009013
20.8585144861240.1733738596090.093475458930.95670373234-0.06152198995260.0173521204632-0.0585964536824-0.1283543812350.05689654158020.127308373204-0.008219548285430.1944059143990.000911657502166-0.08024613148060.009986956849630.0696373320843-0.0002947724153880.003626955963160.0544790772073-0.01173092678680.116588417608-16.2723793307-11.209814173514.0835500956
30.0195803498876-0.0628652960409-0.087356582510.2008602293650.2790674736110.3877501250270.002188254271160.0841878341870.0290299565613-0.17229540623-0.06915072798750.161656153356-0.108872979418-0.165423385072-0.009484856567810.0967457695094-0.00277970001297-0.01942801249630.0966474015639-0.004277652108760.140468569166-13.1199719854-6.933066530254.58556500776
40.09302039408580.02251625078680.05031179824740.06124998276440.06079126631560.1562168618690.01037283988740.06868651451220.0128353852958-0.08987225494290.0232543628241-0.0187844759682-0.04886959600130.01417688909290.01210440908330.09015057454140.00276999356702-0.003619428680080.0577870809407-0.003255713619990.105222264166-3.057192022-8.812525950874.99685370462
50.0271292845284-0.0164428219549-0.02691069324080.0195328365478-0.002575878674390.0641024435230.0384488625539-0.0064494811596-0.02235148686640.0685868085098-0.010014369958-0.154402479296-0.061273117095-0.02505693830730.0004685530278110.0906842457166-0.0188356512476-0.001151789630560.0846066091963-0.005739219223140.1042289098922.12310960088-4.8227214799610.7727957401
60.2440787429880.003554395276730.06632820627780.1650375797650.1072567870580.08645175896830.00416780121526-0.1574271338440.01489656889260.1270044075220.04869761103010.005550293201520.1494564659980.05986048346070.02848658890350.09489753433370.0101094561414-0.004158359902830.0728939757968-0.01791547787140.112775946095-1.69123600201-6.2651956029515.4952460724
70.9676707817370.212241796328-0.03632634043010.0500546314519-0.02436285478920.0822834612801-0.05338637030550.09416886571650.0223815868451-0.004970459966860.03526067782480.01884523372750.0610933056799-0.0130906519406-0.007345852434260.07233925301790.00706739004395-0.009130381434020.0413957333283-0.005670252905520.0983777089597-5.4946408324-21.065618004910.8725698621
80.609673849563-0.278787859762-0.07478311629520.179609350998-0.03275575267080.266143728571-0.0139267209271-0.05241126588190.2130164517790.175923183349-0.04736304891290.1242778944260.061725529517-0.364564848481-0.06770097238570.1728956482940.02158361394740.03093998519310.260667679214-0.02534135608160.134941429467-18.2181274514-15.760985477331.7553154845
90.1700965330380.1196449339760.1974882111490.08434669459660.1391866605530.229443442687-0.07676293318980.0608224120274-0.1099558393420.01798853525910.0400455755425-0.01069861787920.07449008088560.1558643382-0.009311634270370.1463161036540.07357476352330.01046488625060.1725153559810.01354249397650.114776590068-3.41446046956-20.108843069434.2254342722
100.01763382331960.03280409113480.01282268797140.06130308457230.02532142818010.0132523079368-0.0388868679023-0.230641021478-0.1268441244420.290127785680.0346761951582-0.1263365131430.1441367954350.11446070837-0.00048377136430.2176205605820.074049893786-0.01416646490780.2440443273110.01599755273290.139688591488-1.93300090649-16.271333594744.6941665706
110.06704875506660.05491669678230.01247737831410.111473373692-0.03466588237350.03791850597990.0337857450967-0.0252099449549-0.009078418354520.08747947482730.0128600956446-0.00870001801895-0.01714497181010.009157683629860.2552673806910.1318730850510.00311850404428-0.009207908513250.1967184966180.0006421372962260.0466468032872-2.84041859177-9.4406276379546.7004366917
120.09206092106950.01115488659630.02555824096930.05062862559740.05948874941660.07726783906150.1481823151110.08298244867520.09961915748480.0393662726742-0.007788994396540.0759272182771-0.132629181775-0.07397050681960.008039478969060.1940755587370.05366296891210.03308374489340.1738353278290.01637411106210.132591046555-8.7909696173-5.1461375276538.3079019721
130.02942229942420.0161895903785-0.0156136010660.02130746550740.001494210009570.0163877834389-0.070073532483-0.03379506274280.06372182333420.1290425379660.1103112357440.13942792031-0.02460903824-0.266925758236-6.02276120335E-50.2219332298310.06403391986740.03181080281050.2560524508940.02270028432840.161618140104-17.2097431652-15.721581699437.2724425759
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 13 )
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 33 )
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 49 )
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 69 )
5X-RAY DIFFRACTION5chain 'A' and (resid 70 through 74 )
6X-RAY DIFFRACTION6chain 'A' and (resid 75 through 87 )
7X-RAY DIFFRACTION7chain 'A' and (resid 88 through 103 )
8X-RAY DIFFRACTION8chain 'B' and (resid -3 through 13 )
9X-RAY DIFFRACTION9chain 'B' and (resid 14 through 33 )
10X-RAY DIFFRACTION10chain 'B' and (resid 34 through 49 )
11X-RAY DIFFRACTION11chain 'B' and (resid 50 through 60 )
12X-RAY DIFFRACTION12chain 'B' and (resid 61 through 87 )
13X-RAY DIFFRACTION13chain 'B' and (resid 88 through 103 )

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