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- PDB-6h8k: Crystal structure of a variant (Q133C in PSST) of Yarrowia lipoly... -

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Basic information

Entry
Database: PDB / ID: 6h8k
TitleCrystal structure of a variant (Q133C in PSST) of Yarrowia lipolytica complex I
Components
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (Unknown polypeptide) x 33
  • NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
  • NUAM protein
  • NUCM protein
  • NUEM protein
  • NUGM protein
  • Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
KeywordsOXIDOREDUCTASE / Membrane Protein / Respiratory chain / Mitochondrial / NADH:ubiquinone oxidoreductase
Function / homology
Function and homology information


NADH dehydrogenase / NADH dehydrogenase activity / respiratory chain complex I / oxidoreductase activity, acting on NAD(P)H / ubiquinone binding / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding ...NADH dehydrogenase / NADH dehydrogenase activity / respiratory chain complex I / oxidoreductase activity, acting on NAD(P)H / ubiquinone binding / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / respirasome / aerobic respiration / mitochondrial membrane / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / mitochondrion / membrane / metal ion binding
Similarity search - Function
Soluble ligand binding domain / SLBB domain / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. ...Soluble ligand binding domain / SLBB domain / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH dehydrogenase, subunit C / NADH ubiquinone oxidoreductase, F subunit / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH-quinone oxidoreductase, chain M/4 / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 6 / Subunit NUKM of protein NADH:Ubiquinone oxidoreductase ...FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 6 / Subunit NUKM of protein NADH:Ubiquinone oxidoreductase / Subunit NUIM of protein NADH:Ubiquinone oxidoreductase / NUGM protein / NUCM protein / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NUAM protein
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.79 Å
AuthorsWirth, C. / Galemou Yoga, E. / Zickermann, V. / Hunte, C.
Funding support Germany, 2items
OrganizationGrant numberCountry
EXC 294 BIOSS Germany
German Research FoundationZI552/4-1 Germany
CitationJournal: Nat Commun / Year: 2018
Title: Locking loop movement in the ubiquinone pocket of complex I disengages the proton pumps.
Authors: Cabrera-Orefice, A. / Yoga, E.G. / Wirth, C. / Siegmund, K. / Zwicker, K. / Guerrero-Castillo, S. / Zickermann, V. / Hunte, C. / Brandt, U.
History
DepositionAug 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: NADH-ubiquinone oxidoreductase chain 1
2: NADH-ubiquinone oxidoreductase chain 2,NADH dehydrogenase subunit 2
3: NADH-ubiquinone oxidoreductase chain 3
4: NADH-ubiquinone oxidoreductase chain 4
5: NADH-ubiquinone oxidoreductase chain 5
6: NADH-ubiquinone oxidoreductase chain 6
A: NUAM protein
B: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
C: NUCM protein
E: NUEM protein
G: NUGM protein
H: Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
I: Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)
K: Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
L: NADH-ubiquinone oxidoreductase chain 4L
Z: Unknown polypeptide
Y: Unknown polypeptide
U: Unknown polypeptide
X: Unknown polypeptide
W: Unknown polypeptide
V: Unknown polypeptide
T: Unknown polypeptide
S: Unknown polypeptide
R: Unknown polypeptide
Q: Unknown polypeptide
P: Unknown polypeptide
F: Unknown polypeptide
O: Unknown polypeptide
M: Unknown polypeptide
D: Unknown polypeptide
J: Unknown polypeptide
N: Unknown polypeptide
a: Unknown polypeptide
b: Unknown polypeptide
c: Unknown polypeptide
d: Unknown polypeptide
e: Unknown polypeptide
f: Unknown polypeptide
g: Unknown polypeptide
h: Unknown polypeptide
i: Unknown polypeptide
j: Unknown polypeptide
k: Unknown polypeptide
l: Unknown polypeptide
m: Unknown polypeptide
n: Unknown polypeptide
o: Unknown polypeptide
p: Unknown polypeptide
q: Unknown polypeptide
r: Unknown polypeptide
s: Unknown polypeptide
t: Unknown polypeptide
u: Unknown polypeptide
v: Unknown polypeptide
w: Unknown polypeptide
x: Unknown polypeptide
y: Unknown polypeptide
z: Unknown polypeptide
AA: Unknown polypeptide
AB: Unknown polypeptide
AC: Unknown polypeptide
AD: Unknown polypeptide
AE: Unknown polypeptide
AF: Unknown polypeptide
AG: Unknown polypeptide
AH: Unknown polypeptide
AI: Unknown polypeptide
AJ: Unknown polypeptide
AK: Unknown polypeptide
AL: Unknown polypeptide
AM: Unknown polypeptide
AN: Unknown polypeptide
AO: Unknown polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)580,52881
Polymers578,06673
Non-polymers2,4618
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)316.310, 316.310, 819.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules 123456L

#1: Protein NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 37702.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6E8, NADH:ubiquinone reductase (H+-translocating)
#2: Protein NADH-ubiquinone oxidoreductase chain 2,NADH dehydrogenase subunit 2 / NADH dehydrogenase subunit 2


Mass: 46373.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6C8, NADH:ubiquinone reductase (H+-translocating)
#3: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 12351.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6C7, NADH:ubiquinone reductase (H+-translocating)
#4: Protein NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 46528.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6D6, NADH:ubiquinone reductase (H+-translocating)
#5: Protein NADH-ubiquinone oxidoreductase chain 5


Mass: 61395.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9B6D3
#6: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 20175.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6E9, NADH:ubiquinone reductase (H+-translocating)
#15: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 8741.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6D4, NADH:ubiquinone reductase (H+-translocating)

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Protein , 16 types, 16 molecules ABCEGHIKXWVQMJpAA

#7: Protein NUAM protein


Mass: 56416.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUU3, NADH dehydrogenase
#8: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 34323.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9UUU2, NADH dehydrogenase, NADH:ubiquinone reductase (H+-translocating)
#9: Protein NUCM protein


Mass: 43255.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUU1, NADH dehydrogenase
#10: Protein NUEM protein


Mass: 16613.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#11: Protein NUGM protein


Mass: 13497.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUU0, NADH dehydrogenase
#12: Protein Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 13304.138 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#13: Protein Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I) / Subunit NUIM of protein NADH:Ubiquinone oxidoreductase


Mass: 14426.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUT8, NADH dehydrogenase
#14: Protein Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I) / Subunit NUKM of protein NADH:Ubiquinone oxidoreductase


Mass: 16513.170 Da / Num. of mol.: 1 / Mutation: Q133C / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUT7, NADH dehydrogenase
#19: Protein Unknown polypeptide


Mass: 4868.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#20: Protein Unknown polypeptide


Mass: 4613.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#21: Protein Unknown polypeptide


Mass: 5379.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#25: Protein Unknown polypeptide


Mass: 5975.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#29: Protein Unknown polypeptide


Mass: 4358.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#31: Protein Unknown polypeptide


Mass: 5890.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#42: Protein Unknown polypeptide


Mass: 6485.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#47: Protein Unknown polypeptide


Mass: 4954.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)

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Protein/peptide , 25 types, 50 molecules ZrYAFUTmAISAJALRPFfACAHAMOlDNaibcgAEAKAO...

#16: Protein/peptide Unknown polypeptide


Mass: 1464.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#17: Protein/peptide Unknown polypeptide


Mass: 3422.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#18: Protein/peptide Unknown polypeptide


Mass: 869.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#22: Protein/peptide Unknown polypeptide


Mass: 1720.111 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#23: Protein/peptide Unknown polypeptide


Mass: 1635.006 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#24: Protein/peptide Unknown polypeptide


Mass: 4273.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#26: Protein/peptide Unknown polypeptide


Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#27: Protein/peptide
Unknown polypeptide


Mass: 1549.902 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#28: Protein/peptide Unknown polypeptide


Mass: 2145.636 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#30: Protein/peptide Unknown polypeptide


Mass: 2571.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#32: Protein/peptide Unknown polypeptide


Mass: 1294.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#33: Protein/peptide Unknown polypeptide


Mass: 2230.741 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#34: Protein/peptide Unknown polypeptide


Mass: 1890.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#35: Protein/peptide
Unknown polypeptide


Mass: 783.958 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#36: Protein/peptide
Unknown polypeptide


Mass: 1379.692 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#37: Protein/peptide Unknown polypeptide


Mass: 1124.378 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#38: Protein/peptide Unknown polypeptide


Mass: 4017.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#39: Protein/peptide Unknown polypeptide


Mass: 4103.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#40: Protein/peptide Unknown polypeptide


Mass: 1975.426 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#41: Protein/peptide Unknown polypeptide


Mass: 3081.790 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#43: Protein/peptide Unknown polypeptide


Mass: 3847.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#44: Protein/peptide Unknown polypeptide


Mass: 2741.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#45: Protein/peptide Unknown polypeptide


Mass: 954.168 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#46: Protein/peptide Unknown polypeptide


Mass: 698.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
#48: Protein/peptide Unknown polypeptide


Mass: 3337.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)

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Non-polymers , 2 types, 8 molecules

#49: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#50: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4

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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: 5.54 Å3/Da / Density % sol: 77.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: PEG 3350, calcium acetate, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.79→50 Å / Num. obs: 120019 / % possible obs: 99.6 % / Redundancy: 21 % / Biso Wilson estimate: 115.37 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.204 / Net I/σ(I): 13.2
Reflection shellResolution: 3.79→3.99 Å / Mean I/σ(I) obs: 0.7 / CC1/2: 0.439

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wz7

4wz7


Resolution: 3.79→40 Å / Cor.coef. Fo:Fc: 0.787 / Cor.coef. Fo:Fc free: 0.794 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.784
RfactorNum. reflection% reflectionSelection details
Rfree0.363 5829 4.86 %RANDOM
Rwork0.361 ---
obs0.361 120019 77.1 %-
Displacement parametersBiso mean: 164.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.5311 Å20 Å20 Å2
2--0.5311 Å20 Å2
3----1.0622 Å2
Refine analyzeLuzzati coordinate error obs: 1.4 Å
Refinement stepCycle: 1 / Resolution: 3.79→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26641 0 8985 0 35626
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00935941HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2349582HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d9522SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes264HARMONIC2
X-RAY DIFFRACTIONt_gen_planes6051HARMONIC5
X-RAY DIFFRACTIONt_it35941HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.71
X-RAY DIFFRACTIONt_other_torsion22.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion6085SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact39678SEMIHARMONIC4
LS refinement shellResolution: 3.79→3.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 -6.19 %
Rwork0.223 727 -
all0.222 775 -
obs--6.8 %
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)
13.64930.3908-1.6807-0.76520.39271.582-0.0417-0.45970.18810.35660.1297-0.18330.10770.1712-0.08791.0827-0.2532-0.1678-0.1008-0.2497-0.0444-2.9305131.381517.8552
22.7934-0.30440.36831.8682-0.06561.02830.04680.3323-0.08330.1847-0.0990.03440.13830.29340.05230.5273-0.0368-0.3127-0.2670.10860.181446.304839.8107-97.7811
32.11360.66161.72290.47235.22594.8225-0.1-0.0326-0.17440.1130.13430.1909-0.0124-0.0635-0.03430.6502-0.14070.3750.1261-0.0755-0.0999-53.1744127.774330.3169
41.3301-0.91530.1742.23220.550600.03-0.16990.0570.27730.1736-0.40330.0870.0988-0.20360.25640.1643-0.3546-0.09160.0670.447777.92825.6745-95.5817
50.9068-0.3665-0.7382-0.7254-1.78161.9202-0.0248-0.08170.22150.21-0.0806-0.1950.16990.03790.10540.1777-0.41020.2082-0.8659-0.2638-0.9931-23.2405110.8452-36.4563
63.00441.33170.35383.75271.82241.23690.1042-0.32010.04970.2415-0.1332-0.2295-0.15980.11540.02910.3825-0.20750.0445-0.4712-0.0026-0.063119.3469103.0412-87.0598
78.20381.00831.79616.01653.56116.21910.1106-0.06770.1093-0.1079-0.0831-0.1075-0.01250.1282-0.02750.377-0.188-0.15080.1243-0.22450.417926.5438140.9403-40.0191
8-2.2281.58110.18738.3427-1.63887.87880.0319-0.106-0.20070.0559-0.02130.00290.1086-0.0722-0.01060.703-0.25770.0332-0.00640.0445-0.0748-11.938793.0809-22.534
92.4729-2.6022-1.00651.59584.67137.22870.010.00640.0756-0.00450.01740.1349-0.0192-0.1559-0.02740.5863-0.12020.15890.1503-0.12470.1628-49.7893150.457929.8802
10-0.21921.99661.90572.84644.4067.36130.1128-0.16230.03470.2443-0.1571-0.0915-0.4404-0.10680.04430.6565-0.18190.08540.0874-0.1757-0.0462-19.1579132.9915-31.903
11-1.53092.34931.56933.9996-0.585800.1048-0.01010.0868-0.0415-0.0976-0.16030.04570.1097-0.00720.0695-0.24360.0978-0.8676-0.2427-0.6245-3.9132.3229-44.7609
12-0.309-0.33110.01722.07380.35740.2002-0.08570.11580.20120.0614-0.15610.04-0.3917-0.2650.24180.169-0.17530.2038-0.496-0.137-0.2466-8.9525119.8738-79.2273
13-1.84271.33813.92584.2161-1.52221.4259-0.0083-0.12130.14990.1931-0.0998-0.53110.0770.28050.1081-0.0801-0.1047-0.1633-0.63470.0774-0.275417.9424100.7513-88.8421
142.1710.14210.00961.8932-1.28840.25850.0231-0.178300.00530.0995-0.43940.148-0.3255-0.12260.6118-0.2331-0.116-0.00730.03460.241519.377373.9163-93.5654
150.0044-0.0805-0.09170.26580.18410.24280.14320.0952-0.02320.169-0.1766-0.12940.03460.01630.03340.6137-0.1402-0.09740.02860.11270.330428.937167.0994-85.2111
161.040.27210.22773.77590.055200.0574-0.40820.30610.2945-0.1117-0.2981-0.2490.21270.0543-0.1828-0.05940.1798-0.36060.0192-0.41710.0362105.0263-81.992
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ 4|* }
3X-RAY DIFFRACTION3{ B|* }
4X-RAY DIFFRACTION4{ 5|* }
5X-RAY DIFFRACTION5{ C|* }
6X-RAY DIFFRACTION6{ 6|* }
7X-RAY DIFFRACTION7{ E|* }
8X-RAY DIFFRACTION8{ G|* }
9X-RAY DIFFRACTION9{ H|* }
10X-RAY DIFFRACTION10{ I|* }
11X-RAY DIFFRACTION11{ K|* }
12X-RAY DIFFRACTION12{ 1|* }
13X-RAY DIFFRACTION13{ L|* }
14X-RAY DIFFRACTION14{ 2|* }
15X-RAY DIFFRACTION15{ Z|* }
16X-RAY DIFFRACTION16{ 3|* }

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