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- PDB-3cma: The structure of CCA and CCA-Phe-Cap-Bio bound to the large ribos... -

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Basic information

Entry
Database: PDB / ID: 3cma
TitleThe structure of CCA and CCA-Phe-Cap-Bio bound to the large ribosomal subunit of Haloarcula marismortui
Components
  • (50S ribosomal protein ...) x 29
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
  • RNA (5'-R(*CP*CP*(8AN))-3')
  • RNA (5'-R(*CP*CP*A)-3')
KeywordsRIBOSOME / RIBOSOME 50S / PROTEIN-PROTEIN COMPLEX / RNA-RNA COMPLEX / PROTEIN-RNA COMPLEX / PEPTIDYL-tRNA HYDROLYSIS
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / nucleotide binding / DNA repair / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / 50s Ribosomal Protein L19e, Chain O, domain 1 - #10 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Ribosomal Protein L31e; Chain: W; / Ribosomal protein L31 / Nuclear Transport Factor 2; Chain: A, - #80 ...Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / 50s Ribosomal Protein L19e, Chain O, domain 1 - #10 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Ribosomal Protein L31e; Chain: W; / Ribosomal protein L31 / Nuclear Transport Factor 2; Chain: A, - #80 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 - #10 / 3-methyladenine DNA Glycosylase II; Chain A, domain 3 / Ribosomal protein L24 / Ribosomal protein L3; domain 3 / Ribosomal protein L3, domain 3 / Ribosomal protein L15e / Ribosomal protein L15 / Ribosomal Protein L15; Chain: K; domain 2 - #10 / Ribosomal Protein L3; Chain: B; domain 2, / Ribosomal Protein L3; Chain: B; domain 2, - #10 / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / 50s Ribosomal Protein L19e, Chain O, domain 1 / Ribosomal Protein L4; Chain: A; / Ribosomal protein L4/L1 / Helix Hairpins - #310 / 50S ribosomal protein L10, archaea / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Atp Synthase Epsilon Chain; Chain: I; / Ribosomal Protein L24e; Chain: T; / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal protein L19e, archaeal / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L15e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L32e, archaeal / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L6 / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Outer Surface Protein A; domain 3 / Ribosomal protein L7Ae, archaea / Ribosomal Protein L22; Chain A / Ribosomal Protein L30; Chain: A, / Ribosomal protein L24e / SH3 type barrels. - #30 / Ribosomal protein L30/S12 / Aldehyde Oxidoreductase; domain 3 / DNA repair Rad51/transcription factor NusA, alpha-helical / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / N-terminal domain of TfIIb / Helix-hairpin-helix domain / 50S ribosomal protein L10, insertion domain superfamily / Translation factors / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / metallochaperone-like domain / TRASH domain / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L31e, conserved site / Ribosomal protein L37ae / Ribosomal protein L44e signature. / Ribosomal protein L10e signature. / Ribosomal protein L32e, conserved site / RRM (RNA recognition motif) domain / Ribosomal protein L6, conserved site-2 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L19/L19e conserved site / Ribosomal L37ae protein family / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Ribosomal protein L39e, conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L31e
Similarity search - Domain/homology
6-AMINOHEXANOIC ACID / : / : / PHENYLALANINE / STRONTIUM ION / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...6-AMINOHEXANOIC ACID / : / : / PHENYLALANINE / STRONTIUM ION / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL43
Similarity search - Component
Biological speciesHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsSimonovic, M. / Steitz, T.A.
CitationJournal: Rna / Year: 2008
Title: Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA.
Authors: Simonovic, M. / Steitz, T.A.
History
DepositionMar 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_ref / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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 / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_2 / _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_ref.pdbx_seq_one_letter_code / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal protein L2P
B: 50S ribosomal protein L3P
C: 50S ribosomal protein L4P
D: 50S ribosomal protein L5P
E: 50S ribosomal protein L6P
F: 50S ribosomal protein L7Ae
G: 50S ribosomal protein L10E
H: 50S ribosomal protein L10e
I: 50S ribosomal protein L11P
J: 50S ribosomal protein L13P
K: 50S ribosomal protein L14P
L: 50S ribosomal protein L15P
M: 50S ribosomal protein L15e
N: 50S ribosomal protein L18P
O: 50S ribosomal protein L18e
P: 50S ribosomal protein L19e
Q: 50S ribosomal protein L21e
R: 50S ribosomal protein L22P
S: 50S ribosomal protein L23P
T: 50S ribosomal protein L24P
U: 50S ribosomal protein L24e
V: 50S ribosomal protein L29P
W: 50S ribosomal protein L30P
X: 50S ribosomal protein L31e
Y: 50S ribosomal protein L32e
Z: 50S ribosomal protein L37Ae
1: 50S ribosomal protein L37e
2: 50S ribosomal protein L39e
3: 50S ribosomal protein L44E
0: 23S RIBOSOMAL RNA
9: 5S RIBOSOMAL RNA
5: RNA (5'-R(*CP*CP*A)-3')
6: RNA (5'-R(*CP*CP*(8AN))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,495,133339
Polymers1,480,05633
Non-polymers15,077306
Water140,4817798
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)211.316, 297.905, 573.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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50S ribosomal protein ... , 29 types, 29 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZ123

#1: Protein 50S ribosomal protein L2P / Ribosome / Hmal2 / Hl4


Mass: 25354.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20276
#2: Protein 50S ribosomal protein L3P / Ribosome / Hmal3 / Hl1


Mass: 37396.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20279
#3: Protein 50S ribosomal protein L4P / Ribosome / Hmal4 / Hl6


Mass: 26457.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12735
#4: Protein 50S ribosomal protein L5P / Ribosome / Hmal5 / Hl13


Mass: 19551.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14124
#5: Protein 50S ribosomal protein L6P / Ribosome / Hmal6 / Hl10


Mass: 19961.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14135
#6: Protein 50S ribosomal protein L7Ae / Ribosome / Hs6


Mass: 12791.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12743
#7: Protein 50S ribosomal protein L10E / Ribosome / Ribosomal protein L10 / Acidic ribosomal protein P0 homolog / L10E / HMal10


Mass: 37169.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P15825
#8: Protein 50S ribosomal protein L10e / Ribosome / Hmal11


Mass: 19942.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60617
#9: Protein 50S ribosomal protein L11P / Ribosome / Hmal13


Mass: 17097.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14122
#10: Protein 50S ribosomal protein L13P / Ribosome / Hmal14 / Hl27


Mass: 16249.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P29198
#11: Protein 50S ribosomal protein L14P / Ribosome / Hmal15 / Hl9


Mass: 14216.233 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22450
#12: Protein 50S ribosomal protein L15P / Ribosome / 50S ribosomal protein LC12


Mass: 18005.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12737
#13: Protein 50S ribosomal protein L15e / Ribosome / Hmal18 / Hl12


Mass: 22404.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60618
#14: Protein 50S ribosomal protein L18P / Ribosome / Hl29 / L19


Mass: 20640.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14123
#15: Protein 50S ribosomal protein L18e / Ribosome


Mass: 12438.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12733
#16: Protein 50S ribosomal protein L19e / Ribosome / Hmal19 / Hl24


Mass: 16796.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14119
#17: Protein 50S ribosomal protein L21e / Ribosome / Hl31


Mass: 10567.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12734
#18: Protein 50S ribosomal protein L22P / Ribosome / Hmal22 / Hl23


Mass: 16966.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10970
#19: Protein 50S ribosomal protein L23P / Ribosome / Hmal23 / Hl25 / L21


Mass: 9612.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12732
#20: Protein 50S ribosomal protein L24P / Ribosome / Hmal24 / Hl16 / Hl15


Mass: 13670.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10972
#21: Protein 50S ribosomal protein L24e / Ribosome / Hl21/Hl22


Mass: 7364.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14116
#22: Protein 50S ribosomal protein L29P / Ribosome / Hmal29 / Hl33


Mass: 7889.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10971
#23: Protein 50S ribosomal protein L30P / Ribosome / Hmal30 / Hl20 / Hl16


Mass: 17062.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14121
#24: Protein 50S ribosomal protein L31e / Ribosome / L34 / Hl30


Mass: 10384.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P18138
#25: Protein 50S ribosomal protein L32e / Ribosome / Hl5


Mass: 26326.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12736
#26: Protein 50S ribosomal protein L37Ae / Ribosome


Mass: 12900.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60619*PLUS
#27: Protein 50S ribosomal protein L37e / Ribosome / L35e


Mass: 6330.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P32410
#28: Protein/peptide 50S ribosomal protein L39e / Ribosome / Hl39e / Hl46e


Mass: 6133.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22452
#29: Protein 50S ribosomal protein L44E / Ribosome / La / Hla


Mass: 10815.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P32411

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RNA chain , 4 types, 4 molecules 0956

#30: RNA chain 23S RIBOSOMAL RNA /


Mass: 946463.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile)
#31: RNA chain 5S RIBOSOMAL RNA /


Mass: 39303.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 6468293
#32: RNA chain RNA (5'-R(*CP*CP*A)-3')


Mass: 894.612 Da / Num. of mol.: 1 / Source method: obtained synthetically
#33: RNA chain RNA (5'-R(*CP*CP*(8AN))-3')


Mass: 893.627 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 9 types, 8104 molecules

#34: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 93 / Source method: obtained synthetically / Formula: Mg
#35: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#36: Chemical...
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 107 / Source method: obtained synthetically / Formula: Sr
#37: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 75 / Source method: obtained synthetically / Formula: Na
#38: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#39: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#40: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#41: Chemical ChemComp-ACA / 6-AMINOHEXANOIC ACID / AMINOCAPROIC ACID / Aminocaproic acid


Type: peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Comment: inhibitor*YM
#42: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7798 / Source method: isolated from a natural source / Formula: H2O

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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: 3.05 Å3/Da / Density % sol: 59.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: PEG6000, KCL, NH4CL, MGCL2, KACETATE, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG600011
2KCL11
3NH4CL11
4MGCl211
5PEG600012
6KCL12
7NH4CL12
8MGCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 439841 / Num. obs: 439841 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.177 / Χ2: 1.21 / Net I/σ(I): 6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.2 % / Num. unique all: 43390 / Χ2: 1.056 / % possible all: 98.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 2.8→49.79 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 52582.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3937 1 %RANDOM
Rwork0.194 ---
obs-400551 91.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.515 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso mean: 51.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å20 Å2
2--0.67 Å20 Å2
3---1.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.8→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29352 61732 323 7798 99205
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d15.5
X-RAY DIFFRACTIONc_improper_angle_d1.33
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scbond_it1.462
X-RAY DIFFRACTIONc_scangle_it2.312.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.395 556 1 %
Rwork0.349 54639 -
all-55195 -
obs--75.9 %

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