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- PDB-6i7v: Ribosomal protein paralogs bL31 and bL36 -

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Basic information

Entry
Database: PDB / ID: 6i7v
TitleRibosomal protein paralogs bL31 and bL36
Components
  • (30S ribosomal protein ...) x 21
  • (50S ribosomal protein ...) x 31
  • 16S ribosmal RNA
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 23S ribsomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / Protein biosynthesis / ribosomes / paralog / RNA / peptidyl / 30S / 70S / 16S / ribosomal subunit
Function / homologyRibosomal protein L4 domain superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L36 superfamily ...Ribosomal protein L4 domain superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Ribosomal protein L25 / Ribosomal protein L21-like / Ribosomal protein L31 type B / Ribosomal protein S20 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / 30s ribosomal protein S13, C-terminal / Ribosomal protein S11 superfamily / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein L19 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein S21 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L28/L24 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein S10 domain / Ribosomal protein L28/L24 / Ribosomal protein S7p/S5e / Ribosomal protein L9, N-terminal / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L9, C-terminal / Ribosomal protein L16, conserved site / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25, short-form / Ribosomal protein L6, alpha-beta domain / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S16 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L13, conserved site / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L5 domain superfamily / Ribosomal protein L2, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L35 / Ribosomal protein L18e/L15P / Ribosomal protein L34, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein S12/S23 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L3, conserved site / KH domain / Ribosomal protein S12 signature. / Ribosomal protein S11 signature. / Ribosomal protein S8 signature. / Ribosomal protein S7 signature. / Ribosomal protein L23 signature. / Ribosomal protein L14 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L9, C-terminal domain / Ribosomal protein S18 signature. / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal L32p protein family / Ribosomal protein S20
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.9 Å resolution
AuthorsPulk, A. / Cate, J.H.D. / Remme, J. / Lilleorg, S. / Reier, K. / Peil, L. / Liiv, A. / Tammsalu, T.
CitationJournal: Biochimie / Year: 2018
Title: Bacterial ribosome heterogeneity: Changes in ribosomal protein composition during transition into stationary growth phase.
Authors: Lilleorg, S. / Reier, K. / Pulk, A. / Liiv, A. / Tammsalu, T. / Peil, L. / Cate, J.D. / Remme, J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 19, 2018 / Release: Dec 5, 2018

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: 16S ribosmal RNA
BA: 16S ribosomal RNA
DA: 23S ribosomal RNA
CA: 23S ribsomal RNA
DB: 5S ribosomal RNA
CB: 5S ribosomal RNA
AB: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AU: 30S ribosomal protein S21
BB: 30S ribosomal protein S2
BC: 30S ribosomal protein S3
BD: 30S ribosomal protein S4
BE: 30S ribosomal protein S5
BF: 30S ribosomal protein S6
BG: 30S ribosomal protein S7
BH: 30S ribosomal protein S8
BI: 30S ribosomal protein S9
BJ: 30S ribosomal protein S10
BK: 30S ribosomal protein S11
BL: 30S ribosomal protein S12
BM: 30S ribosomal protein S13
BN: 30S ribosomal protein S14
BO: 30S ribosomal protein S15
BP: 30S ribosomal protein S16
BQ: 30S ribosomal protein S17
BR: 30S ribosomal protein S18
BS: 30S ribosomal protein S19
BT: 30S ribosomal protein S20
BU: 30S ribosomal protein S21
CC: 50S ribosomal protein L2
CD: 50S ribosomal protein L3
CE: 50S ribosomal protein L4
CF: 50S ribosomal protein L5
CG: 50S ribosomal protein L6
CH: 50S ribosomal protein L9
CJ: 50S ribosomal protein L11
CK: 50S ribosomal protein L13
CL: 50S ribosomal protein L14
CM: 50S ribosomal protein L15
CN: 50S ribosomal protein L16
CO: 50S ribosomal protein L17
CP: 50S ribosomal protein L18
CQ: 50S ribosomal protein L19
CR: 50S ribosomal protein L20
CS: 50S ribosomal protein L21
CT: 50S ribosomal protein L22
CU: 50S ribosomal protein L23
CV: 50S ribosomal protein L24
CW: 50S ribosomal protein L25
CX: 50S ribosomal protein L27
CY: 50S ribosomal protein L28
CZ: 50S ribosomal protein L29
C0: 50S ribosomal protein L30
C1: 50S ribosomal protein L32
C2: 50S ribosomal protein L33
C3: 50S ribosomal protein L34
C4: 50S ribosomal protein L35
C5: 50S ribosomal protein L36 2
DC: 50S ribosomal protein L2
DD: 50S ribosomal protein L3
DE: 50S ribosomal protein L4
DF: 50S ribosomal protein L5
DG: 50S ribosomal protein L6
DH: 50S ribosomal protein L9
DJ: 50S ribosomal protein L11
DK: 50S ribosomal protein L13
DL: 50S ribosomal protein L14
DM: 50S ribosomal protein L15
DN: 50S ribosomal protein L16
DO: 50S ribosomal protein L17
DP: 50S ribosomal protein L18
DQ: 50S ribosomal protein L19
DR: 50S ribosomal protein L20
DS: 50S ribosomal protein L21
DT: 50S ribosomal protein L22
DU: 50S ribosomal protein L23
DV: 50S ribosomal protein L24
DW: 50S ribosomal protein L25
DX: 50S ribosomal protein L27
DY: 50S ribosomal protein L28
DZ: 50S ribosomal protein L29
D0: 50S ribosomal protein L30
D1: 50S ribosomal protein L32
D2: 50S ribosomal protein L33
D3: 50S ribosomal protein L34
D4: 50S ribosomal protein L35
D5: 50S ribosomal protein L36 2
D7: 50S ribosomal protein L31 type B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,257,120621
Polyers4,238,840105
Non-polymers18,279516
Water117,9986550
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)539860
ΔGint (kcal/M)-4335
Surface area (Å2)1527230
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)212.020, 434.570, 623.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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RNA chain , 5 types, 6 molecules AABADACADBCB

#1: RNA chain 16S ribosmal RNA


Mass: 497075.812 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1370526461
#2: RNA chain 16S ribosomal RNA /


Mass: 496892.375 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1370526449
#3: RNA chain 23S ribosomal RNA /


Mass: 941505.375 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1109114233
#4: RNA chain 23S ribsomal RNA


Mass: 941612.375 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1109114233
#5: RNA chain 5S ribosomal RNA /


Mass: 38483.926 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1435226024

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30S ribosomal protein ... , 21 types, 40 molecules ABBBACBCADBDAEBEAFBFAGBGAHBHAIBIAJBJAKBKALAMBMANBNAOBOAPBPAQ...

#6: Protein/peptide 30S ribosomal protein S2 / / Small ribosomal subunit protein uS2


Mass: 24253.943 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V0
#7: Protein/peptide 30S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 23078.785 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V3
#8: Protein/peptide 30S ribosomal protein S4 / / Small ribosomal subunit protein uS4


Mass: 23383.002 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V8
#9: Protein/peptide 30S ribosomal protein S5 / / Small ribosomal subunit protein uS5


Mass: 15804.282 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W1
#10: Protein/peptide 30S ribosomal protein S6 / / Small ribosomal subunit protein bS6


Mass: 11669.371 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358
#11: Protein/peptide 30S ribosomal protein S7 / / Small ribosomal subunit protein uS7


Mass: 16861.523 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359
#12: Protein/peptide 30S ribosomal protein S8 / / Small ribosomal subunit protein uS8


Mass: 14015.361 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W7
#13: Protein/peptide 30S ribosomal protein S9 / / Small ribosomal subunit protein uS9


Mass: 14554.882 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7X3
#14: Protein/peptide 30S ribosomal protein S10 / / Small ribosomal subunit protein uS10


Mass: 11196.988 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R5
#15: Protein/peptide 30S ribosomal protein S11 / / Small ribosomal subunit protein uS11


Mass: 12487.200 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9
#16: Protein/peptide 30S ribosomal protein S12 / / Small ribosomal subunit protein uS12


Mass: 13683.053 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3
#17: Protein/peptide 30S ribosomal protein S13 / / Small ribosomal subunit protein uS13


Mass: 12625.753 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S9
#18: Protein/peptide 30S ribosomal protein S14 / / Small ribosomal subunit protein uS14


Mass: 11475.364 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG59
#19: Protein/peptide 30S ribosomal protein S15 /


Mass: 10188.687 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SSQ8
#20: Protein/peptide 30S ribosomal protein S16 / / Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T3
#21: Protein/peptide 30S ribosomal protein S17 / / Small ribosomal subunit protein uS17


Mass: 9263.946 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG63
#22: Protein/peptide 30S ribosomal protein S18 / / Small ribosomal subunit protein bS18


Mass: 6466.477 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T7
#23: Protein/peptide 30S ribosomal protein S19 / / Small ribosomal subunit protein uS19


Mass: 9057.626 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U3
#24: Protein/peptide 30S ribosomal protein S20 / / Small ribosomal subunit protein bS20


Mass: 9506.190 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U7
#25: Protein/peptide 30S ribosomal protein S21 / / Small ribosomal subunit protein bS21


Mass: 6433.499 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68679
#26: Protein/peptide 30S ribosomal protein S12 / / Small ribosomal subunit protein uS12


Mass: 13636.961 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3

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50S ribosomal protein ... , 31 types, 59 molecules CCDCCDCEDECFDFCGDGCHDHCJDJCKDKCLDLCMDMCNDNCODOCPDPCQDQCRDRCS...

#27: Protein/peptide 50S ribosomal protein L2 / / Large ribosomal subunit protein uL2


Mass: 29663.244 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60422
#28: Protein/peptide 50S ribosomal protein L3 / / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60438
#29: Protein/peptide 50S ribosomal protein L4 / / Large ribosomal subunit protein uL4


Mass: 22121.566 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60723
#30: Protein/peptide 50S ribosomal protein L5 / / Large ribosomal subunit protein uL5


Mass: 20073.234 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P62399
#31: Protein/peptide 50S ribosomal protein L6 / / Large ribosomal subunit protein uL6


Mass: 18801.598 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG55
#32: Protein/peptide 50S ribosomal protein L9 / / Large ribosomal subunit protein bL9


Mass: 15674.877 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R1
#33: Protein/peptide 50S ribosomal protein L11 / / Large ribosomal subunit protein uL11


Mass: 14763.165 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7J7
#34: Protein/peptide 50S ribosomal protein L13 / / Large ribosomal subunit protein uL13


Mass: 16050.606 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AA10
#35: Protein/peptide 50S ribosomal protein L14 / / Large ribosomal subunit protein uL14


Mass: 13565.067 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY3
#36: Protein/peptide 50S ribosomal protein L15 / / Large ribosomal subunit protein uL15


Mass: 15008.471 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02413
#37: Protein/peptide 50S ribosomal protein L16 / / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY7
#38: Protein/peptide 50S ribosomal protein L17 / / Large ribosomal subunit protein bL17


Mass: 13721.938 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG44
#39: Protein/peptide 50S ribosomal protein L18 / / Large ribosomal subunit protein uL18


Mass: 12794.668 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0C018
#40: Protein/peptide 50S ribosomal protein L19 / / Large ribosomal subunit protein bL19


Mass: 13028.082 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7K6
#41: Protein/peptide 50S ribosomal protein L20 / / Large ribosomal subunit protein bL20


Mass: 13396.828 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L3
#42: Protein/peptide 50S ribosomal protein L21 / / Large ribosomal subunit protein bL21


Mass: 11586.374 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG48
#43: Protein/peptide 50S ribosomal protein L22 / / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P61175
#44: Protein/peptide 50S ribosomal protein L23 / / Large ribosomal subunit protein uL23


Mass: 10546.472 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#45: Protein/peptide 50S ribosomal protein L24 / / Large ribosomal subunit protein uL24


Mass: 11078.874 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60624
#46: Protein/peptide 50S ribosomal protein L25 / / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68919
#47: Protein/peptide 50S ribosomal protein L27 / / Large ribosomal subunit protein bL27


Mass: 8275.498 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L8
#48: Protein/peptide 50S ribosomal protein L28 / / Large ribosomal subunit protein bL28


Mass: 8896.354 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M2
#49: Protein/peptide 50S ribosomal protein L29 / / Large ribosomal subunit protein uL29


Mass: 7155.267 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M6
#50: Protein/peptide 50S ribosomal protein L30 / / Large ribosomal subunit protein uL30


Mass: 6423.625 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG51
#51: Protein/peptide 50S ribosomal protein L32 / / Large ribosomal subunit protein bL32


Mass: 6332.249 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N4
#52: Protein/peptide 50S ribosomal protein L33 / / Large ribosomal subunit protein bL33


Mass: 5885.919 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N9
#53: Protein/peptide 50S ribosomal protein L34 / / Large ribosomal subunit protein bL34


Mass: 5397.463 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7P5
#54: Protein/peptide 50S ribosomal protein L35 / / Large ribosomal subunit protein bL35 / Ribosomal protein A


Mass: 7181.835 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q1
#55: Protein/peptide 50S ribosomal protein L36 2 / Ribosome / Large ribosomal subunit protein bL36-B


Mass: 5326.496 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q2EEQ2
#56: Protein/peptide 50S ribosomal protein L3 / / Large ribosomal subunit protein uL3


Mass: 22291.562 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60438
#57: Protein/peptide 50S ribosomal protein L31 type B / Ribosome / Large ribosomal subunit protein bL31-B


Mass: 7778.693 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N1

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Non-polymers , 12 types, 7066 molecules

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


Mass: 24.305 Da / Num. of mol.: 453 / Formula: Mg / Magnesium
#59: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 8 / Formula: C6H14O4 / Triethylene glycol
#60: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 13 / Formula: C6H14O2 / 2-Methyl-2,4-pentanediol
#61: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Formula: C8H18O5 / Polyethylene glycol / Comment: precipitant for crystallization *YM
#62: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 3 / Formula: C7H19N3 / Spermidine
#63: Chemical
ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 7 / Formula: C4H12N2 / Putrescine
#64: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Formula: C10H22O6 / Polyethylene glycol / Comment: precipitant for crystallization *YM
#65: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Formula: C2H4O2 / Acetic acid
#66: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Formula: C4H10O3
#67: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Formula: C2H6O2 / Ethylene glycol
#68: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 1 / Formula: C5H5N5O / Guanine
#69: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6550 / Formula: H2O / Water

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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: 3.39 / Density percent sol: 63.73 %
Crystal growTemp: 291 K / Method: microbatch / pH: 6.5 / Details: PEG8k, MPD, KSCN

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Data collection

Diffraction
IDMean temperatureCrystal IDSerial crystal experiment
12911N
22911N
Source
SourceTypeSynchrotron siteBeamlineIdWavelength
SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.111.1
SYNCHROTRONALS BEAMLINE 12.3.1ALS12.3.121.1
Detector
TypeIdDetectorCollection date
ADSC QUANTUM 3151CCD2013-10-03
ADSC QUANTUM 3152CCD2013-11-16
Radiation
IdDiffraction protocolMonochromatic or laue m lScattering typeWavelength ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelengthRelative weight
11.11.0
21.11.0
ReflectionB iso Wilson estimate: 46.54 / D resolution high: 2.8 / D resolution low: 69.324 / Number obs: 1077740 / Rmerge I obs: 0.208 / NetI over sigmaI: 6.71 / Redundancy: 6.39 % / Percent possible obs: 77.3
Reflection shellRmerge I obs: 1.686 / Highest resolution: 2.8 / Lowest resolution: 2.9 / MeanI over sigI obs: 0.23 / Redundancy: 1.03 % / Percent possible all: 5.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YBB
Overall SU ML: 0.404 / Cross valid method: FREE R-VALUE / Sigma F: 2.01 / Overall phase error: 25.279
Solvent computationSolvent shrinkage radii: 0.9 / Solvent vdw probe radii: 1.11
Displacement parametersB iso mean: 124.1
Least-squares processR factor R free: 0.255 / R factor R work: 0.186 / R factor obs: 0.186 / Highest resolution: 2.9 / Lowest resolution: 69.32 / Number reflection R free: 5351 / Number reflection obs: 1070140 / Percent reflection R free: 0.5 / Percent reflection obs: 85.2
Refine hist #LASTHighest resolution: 2.9 / Lowest resolution: 69.32
Number of atoms included #LASTProtein: 90042 / Nucleic acid: 195305 / Ligand: 940 / Solvent: 6550 / Total: 292837
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013310512
X-RAY DIFFRACTIONf_angle_d2.001464205
X-RAY DIFFRACTIONf_dihedral_angle_d19.059165978
X-RAY DIFFRACTIONf_chiral_restr0.08159215
X-RAY DIFFRACTIONf_plane_restr0.01424946
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.90000.30870.23123.00361883735430.00
3.00360.28740.24413.12393496947856.00
3.12390.30790.23483.266153210588685.00
3.26610.29630.22423.438357511440092.00
3.43830.27750.21023.653758811694194.00
3.65370.26530.18863.935860211978696.00
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