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- PDB-2wss: The structure of the membrane extrinsic region of bovine ATP synthase -

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Basic information

Entry
Database: PDB / ID: 2wss
TitleThe structure of the membrane extrinsic region of bovine ATP synthase
Components
  • (ATP SYNTHASE SUBUNIT ...) x 8
  • ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL
KeywordsHYDROLASE / HYDROGEN ION TRANSPORT / ATP SYNTHESIS / PHOSPHOPROTEIN / UBL CONJUGATION / TRANSIT PEPTIDE / NUCLEOTIDE-BINDING / ACETYLATION / ATP-BINDING / ION TRANSPORT / MITOCHONDRION / PYRROLIDONE CARBOXYLIC ACID / TRANSPORT
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) ...Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / aerobic respiration / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial inner membrane / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2210 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #200 / N-terminal domain of the delta subunit of the F1F0-ATP synthase / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP synthase delta/epsilon subunit, C-terminal domain / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / Atp Synthase Epsilon Chain; Chain: I; / ATP synthase alpha/beta chain, C-terminal domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2210 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #200 / N-terminal domain of the delta subunit of the F1F0-ATP synthase / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP synthase delta/epsilon subunit, C-terminal domain / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / Atp Synthase Epsilon Chain; Chain: I; / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / Pyruvate Kinase; Chain: A, domain 1 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / Peroxidase; domain 1 / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Elongation Factor Tu (Ef-tu); domain 3 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Helix Hairpins / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ATP synthase subunit beta, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRees, D.M. / Leslie, A.G.W. / Walker, J.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The Structure of the Membrane Extrinsic Region of Bovine ATP Synthase
Authors: Rees, D.M. / Leslie, A.G.W. / Walker, J.E.
History
DepositionSep 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 0-STRANDED BARREL THIS IS REPRESENTED BY A 1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "JA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
B: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
C: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
D: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
E: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
F: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
G: ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
H: ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
I: ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
J: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
K: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
L: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
M: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
N: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
O: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
P: ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
Q: ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
R: ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
S: ATP SYNTHASE SUBUNIT O, MITOCHONDRIAL
T: ATP SYNTHASE SUBUNIT B, MITOCHONDRIAL
U: ATP SYNTHASE SUBUNIT D, MITOCHONDRIAL
V: ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL
W: ATP SYNTHASE SUBUNIT O, MITOCHONDRIAL
X: ATP SYNTHASE SUBUNIT B, MITOCHONDRIAL
Z: ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)851,82745
Polymers846,68025
Non-polymers5,14720
Water0
1
A: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
B: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
C: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
D: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
E: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
F: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
G: ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
H: ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
I: ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
S: ATP SYNTHASE SUBUNIT O, MITOCHONDRIAL
T: ATP SYNTHASE SUBUNIT B, MITOCHONDRIAL
U: ATP SYNTHASE SUBUNIT D, MITOCHONDRIAL
V: ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)432,61023
Polymers430,03713
Non-polymers2,57410
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54520 Å2
ΔGint-239.9 kcal/mol
Surface area171300 Å2
MethodPISA
2
J: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
K: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
L: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
M: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
N: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
O: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
P: ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
Q: ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
R: ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
W: ATP SYNTHASE SUBUNIT O, MITOCHONDRIAL
X: ATP SYNTHASE SUBUNIT B, MITOCHONDRIAL
Z: ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)419,21722
Polymers416,64412
Non-polymers2,57410
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44760 Å2
ΔGint-222.4 kcal/mol
Surface area161110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.244, 231.245, 286.361
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27
18
28
19
29
110
210
111
211

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A RESID 30:500
211CHAIN J AND RESID 30:500
112CHAIN B RESID 30:500
212CHAIN K AND RESID 30:500
113CHAIN C RESID 30:500
213CHAIN L AND RESID 30:500
114CHAIN D RESID 30:475
214CHAIN M AND RESID 30:475
115CHAIN E RESID 30:475
215CHAIN N AND RESID 30:400
116CHAIN F RESID 30:475
216CHAIN O AND RESID 30:400
117CHAIN G RESID 1:270
217CHAIN P AND RESID 1:270
118CHAIN H RESID 15:145
218CHAIN Q AND RESID 15:145
119CHAIN I RESID 1:45
219CHAIN R AND RESID 1:45
1110CHAIN S RESID 20:100
2110CHAIN W AND RESID 20:100
1111CHAIN T RESID 30:475
2111CHAIN X AND RESID 30:400

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11

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Components

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ATP SYNTHASE SUBUNIT ... , 8 types, 23 molecules ABCJKLDEFMNOGPHQIRSWTXU

#1: Protein
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL /


Mass: 55301.207 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P19483
#2: Protein
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL /


Mass: 51757.836 Da / Num. of mol.: 6 / Fragment: RESIDUES 47-528 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle)
References: UniProt: P00829, H+-transporting two-sector ATPase
#3: Protein ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL / / F-ATPASE GAMMA SUBUNIT


Mass: 30185.674 Da / Num. of mol.: 2 / Fragment: HEART ISOFORM, RESIDUES 26-297 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P05631
#4: Protein ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL / / F-ATPASE DELTA SUBUNIT


Mass: 15074.813 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P05630
#5: Protein/peptide ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL /


Mass: 5662.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) BOS TAURUS (cattle) / References: UniProt: P05632
#6: Protein ATP SYNTHASE SUBUNIT O, MITOCHONDRIAL / / OLIGOMYCIN SENSITIVITY CONFERRAL PROTEIN / OSCP


Mass: 21364.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Plasmid: PRUN/B99-214D1-120F6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P13621
#7: Protein ATP SYNTHASE SUBUNIT B, MITOCHONDRIAL /


Mass: 14113.428 Da / Num. of mol.: 2 / Fragment: RESIDUES 141-256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Plasmid: PRUN/B99-214D1-120F6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P13619
#8: Protein ATP SYNTHASE SUBUNIT D, MITOCHONDRIAL /


Mass: 13393.225 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Plasmid: PRUN/B99-214D1-120F6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P13620

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Protein , 1 types, 2 molecules VZ

#9: Protein ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL / ATPASE SUBUNIT F6


Mass: 9064.869 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Plasmid: PRUN/OSCP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P02721

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Non-polymers , 3 types, 20 molecules

#10: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#11: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#12: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Sequence detailsTHE SEQUENCE CONFLICT S->G HAS BEEN DESCRIBED BY WALKER, J.E ET AL (PUBMED ID: 2864455).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.47 % / Description: NONE
Crystal growMethod: microbatch / Details: MICROBATCH UNDER OIL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→41.78 Å / Num. obs: 172437 / % possible obs: 99.7 % / Observed criterion σ(I): 1.5 / Redundancy: 3.7 % / Biso Wilson estimate: 75.93 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.4
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CK3

2ck3


Resolution: 3.2→41.77 Å / SU ML: 0.39 / σ(F): 0.01 / Phase error: 27.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 8036 4.99 %
Rwork0.217 --
obs0.22 161021 93.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.13 Å2 / ksol: 0.28 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5001 Å20 Å2-0 Å2
2--5.5726 Å2-0 Å2
3----6.0727 Å2
Refinement stepCycle: LAST / Resolution: 3.2→41.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms54633 0 312 0 54945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01155766
X-RAY DIFFRACTIONf_angle_d1.34375383
X-RAY DIFFRACTIONf_dihedral_angle_d20.02520993
X-RAY DIFFRACTIONf_chiral_restr0.0798740
X-RAY DIFFRACTIONf_plane_restr0.0089729
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3595X-RAY DIFFRACTIONPOSITIONAL
12J3595X-RAY DIFFRACTIONPOSITIONAL0.058
21B3536X-RAY DIFFRACTIONPOSITIONAL
22K3536X-RAY DIFFRACTIONPOSITIONAL0.051
31C3595X-RAY DIFFRACTIONPOSITIONAL
32L3595X-RAY DIFFRACTIONPOSITIONAL0.043
41D3388X-RAY DIFFRACTIONPOSITIONAL
42M3388X-RAY DIFFRACTIONPOSITIONAL0.047
51E2793X-RAY DIFFRACTIONPOSITIONAL
52N2793X-RAY DIFFRACTIONPOSITIONAL0.05
61F2789X-RAY DIFFRACTIONPOSITIONAL
62O2789X-RAY DIFFRACTIONPOSITIONAL0.047
71G2014X-RAY DIFFRACTIONPOSITIONAL
72P2014X-RAY DIFFRACTIONPOSITIONAL0.037
81H970X-RAY DIFFRACTIONPOSITIONAL
82Q970X-RAY DIFFRACTIONPOSITIONAL0.018
91I353X-RAY DIFFRACTIONPOSITIONAL
92R353X-RAY DIFFRACTIONPOSITIONAL0.019
101S625X-RAY DIFFRACTIONPOSITIONAL
102W625X-RAY DIFFRACTIONPOSITIONAL0.024
111T336X-RAY DIFFRACTIONPOSITIONAL
112X336X-RAY DIFFRACTIONPOSITIONAL0.022
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.23640.43292280.38384344X-RAY DIFFRACTION80
3.2364-3.27440.3982340.3554330X-RAY DIFFRACTION81
3.2744-3.31430.38822330.35014474X-RAY DIFFRACTION82
3.3143-3.35630.39242110.34224610X-RAY DIFFRACTION84
3.3563-3.40040.40362500.30694586X-RAY DIFFRACTION85
3.4004-3.4470.33722530.30014743X-RAY DIFFRACTION87
3.447-3.49620.34962500.29054836X-RAY DIFFRACTION89
3.4962-3.54840.35982490.27164868X-RAY DIFFRACTION90
3.5484-3.60380.33292660.26294989X-RAY DIFFRACTION91
3.6038-3.66280.34192530.24694953X-RAY DIFFRACTION92
3.6628-3.72590.30262560.23665027X-RAY DIFFRACTION92
3.7259-3.79360.27662460.2235113X-RAY DIFFRACTION93
3.7936-3.86660.28222620.21025073X-RAY DIFFRACTION94
3.8666-3.94540.27642850.20385174X-RAY DIFFRACTION95
3.9454-4.03120.24942680.18745146X-RAY DIFFRACTION95
4.0312-4.12480.25462790.19865238X-RAY DIFFRACTION96
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