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PDBsum entry 470d

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RNA PDB id
470d
Jmol
Contents
Ligands
C43-G48-C43-G48-
A44-A44-U36-U36-
C43-G48-C43-G48
×2
Metals
_MG ×2
Waters ×123
HEADER    RNA                                     29-APR-99   470D
TITLE     CRYSTAL STRUCTURE AND IMPROVED ANTISENSE PROPERTIES OF 2'-O-(2-
TITLE    2 METHOXYETHYL)-RNA
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: RNA (5'-R(*(C43)P*(G48)P*(C43)P*(G48)P*(A44)P*(A44)P*(U36)
COMPND   3 P*(U36)P*(C43)P*(G48)P*(C43)P*(G48))-3');
COMPND   4 CHAIN: A, B;
COMPND   5 ENGINEERED: YES;
COMPND   6 OTHER_DETAILS: O2* OF EACH RIBOSE MODIFIED BY METHOXYETHYL
SOURCE    MOL_ID: 1;
SOURCE   2 SYNTHETIC: YES
KEYWDS    2'-O-(2-METHOXYETHYL) RIBOSE, RNA DODECAMER DUPLEX, RIBONUCLEIC ACID,
KEYWDS   2 RNA
EXPDTA    X-RAY DIFFRACTION
AUTHOR    M.TEPLOVA,G.MINASOV,V.TERESHKO,G.INAMATI,P.D.COOK,M.EGLI
REVDAT   6   27-FEB-13 470D    1       HETATM
REVDAT   5   16-JAN-13 470D    1       HETATM
REVDAT   4   16-NOV-11 470D    1       VERSN  HETATM
REVDAT   3   24-FEB-09 470D    1       VERSN
REVDAT   2   01-APR-03 470D    1       JRNL
REVDAT   1   12-MAY-99 470D    0
JRNL        AUTH   M.TEPLOVA,G.MINASOV,V.TERESHKO,G.B.INAMATI,P.D.COOK,
JRNL        AUTH 2 M.MANOHARAN,M.EGLI
JRNL        TITL   CRYSTAL STRUCTURE AND IMPROVED ANTISENSE PROPERTIES OF
JRNL        TITL 2 2'-O-(2-METHOXYETHYL)-RNA.
JRNL        REF    NAT.STRUCT.BIOL.              V.   6   535 1999
JRNL        REFN                   ISSN 1072-8368
JRNL        PMID   10360355
JRNL        DOI    10.1038/9304
REMARK   2
REMARK   2 RESOLUTION.    1.95 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : X-PLOR 3.851
REMARK   3   AUTHORS     : BRUNGER
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 8.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 2.000
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 85.6
REMARK   3   NUMBER OF REFLECTIONS             : 4359
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
REMARK   3   R VALUE            (WORKING SET) : 0.209
REMARK   3   FREE R VALUE                     : 0.257
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.000
REMARK   3   FREE R VALUE TEST SET COUNT      : NULL
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : NULL
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : NULL
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : NULL
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : NULL
REMARK   3   BIN R VALUE           (WORKING SET) : NULL
REMARK   3   BIN FREE R VALUE                    : NULL
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : NULL
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 0
REMARK   3   NUCLEIC ACID ATOMS       : 602
REMARK   3   HETEROGEN ATOMS          : 2
REMARK   3   SOLVENT ATOMS            : 123
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : NULL
REMARK   3    B22 (A**2) : NULL
REMARK   3    B33 (A**2) : NULL
REMARK   3    B12 (A**2) : NULL
REMARK   3    B13 (A**2) : NULL
REMARK   3    B23 (A**2) : NULL
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL
REMARK   3   ESD FROM SIGMAA              (A) : NULL
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : 0.011
REMARK   3   BOND ANGLES            (DEGREES) : 1.88
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  NCS MODEL : NULL
REMARK   3
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  PARAMETER FILE  1  : NULL
REMARK   3  TOPOLOGY FILE  1   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 470D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 03-APR-98
REMARK 200  TEMPERATURE           (KELVIN) : 120.0
REMARK 200  PH                             : 7.5
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : N
REMARK 200  RADIATION SOURCE               : ROTATING ANODE
REMARK 200  BEAMLINE                       : NULL
REMARK 200  X-RAY GENERATOR MODEL          : RIGAKU RU200
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : MIRRORS
REMARK 200
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU RAXIS IIC
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 4996
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.950
REMARK 200  RESOLUTION RANGE LOW       (A) : 20.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 97.1
REMARK 200  DATA REDUNDANCY                : 4.500
REMARK 200  R MERGE                    (I) : 0.05800
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): NULL
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: DROPLETS CONTAINING 2MM
REMARK 280  OLIGONUCLEOTIDE, 50 MM MGCL2, 50 MM NA HEPES PH 7.5, 15% PEG 400,
REMARK 280  AGAINST 1 ML OF RESERVOIR SOLUTION CONTAINING 100 MM MGCL2, 100
REMARK 280  MM NA HEPES PH 7.5, 30% PEG 400, VAPOR DIFFUSION, HANGING DROP,
REMARK 280  TEMPERATURE 295K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,Y,-Z
REMARK 290       3555   X+1/2,Y+1/2,Z
REMARK 290       4555   -X+1/2,Y+1/2,-Z
REMARK 290
REMARK 290     WHERE NNN -> OPERATOR NUMBER
REMARK 290           MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   3  1.000000  0.000000  0.000000       21.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       17.80000
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000       21.00000
REMARK 290   SMTRY2   4  0.000000  1.000000  0.000000       17.80000
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375      HOH A 113  LIES ON A SPECIAL POSITION.
REMARK 375 MG    MG A 106  LIES ON A SPECIAL POSITION.
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              MG A 100  MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH B 104   O
REMARK 620 2 HOH B 103   O    90.2
REMARK 620 3 HOH A 101   O    87.7 177.6
REMARK 620 4 HOH B 102   O    95.2  94.9  86.4
REMARK 620 5 HOH A 105   O   175.4  92.3  89.7  88.4
REMARK 620 N                    1     2     3     4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              MG A 106  MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 108   O
REMARK 620 2 HOH A 109   O    89.7
REMARK 620 3 HOH A 107   O    91.0  93.9
REMARK 620 N                    1     2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 100
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 106
DBREF  470D A    1    12  PDB    470D     470D             1     12
DBREF  470D B   13    24  PDB    470D     470D            13     24
SEQRES   1 A   12  C43 G48 C43 G48 A44 A44 U36 U36 C43 G48 C43 G48
SEQRES   1 B   12  C43 G48 C43 G48 A44 A44 U36 U36 C43 G48 C43 G48
MODRES 470D C43 A    1    C
MODRES 470D G48 A    2    G
MODRES 470D C43 A    3    C
MODRES 470D G48 A    4    G
MODRES 470D A44 A    5    A
MODRES 470D A44 A    6    A
MODRES 470D U36 A    7    U
MODRES 470D U36 A    8    U
MODRES 470D C43 A    9    C
MODRES 470D G48 A   10    G
MODRES 470D C43 A   11    C
MODRES 470D G48 A   12    G
MODRES 470D C43 B   13    C
MODRES 470D G48 B   14    G
MODRES 470D C43 B   15    C
MODRES 470D G48 B   16    G
MODRES 470D A44 B   17    A
MODRES 470D A44 B   18    A
MODRES 470D U36 B   19    U
MODRES 470D U36 B   20    U
MODRES 470D C43 B   21    C
MODRES 470D G48 B   22    G
MODRES 470D C43 B   23    C
MODRES 470D G48 B   24    G
HET    C43  A   1      21
HET    G48  A   2      27
HET    C43  A   3      24
HET    G48  A   4      27
HET    A44  A   5      26
HET    A44  A   6      26
HET    U36  A   7      24
HET    U36  A   8      24
HET    C43  A   9      24
HET    G48  A  10      27
HET    C43  A  11      24
HET    G48  A  12      27
HET    C43  B  13      21
HET    G48  B  14      27
HET    C43  B  15      24
HET    G48  B  16      27
HET    A44  B  17      26
HET    A44  B  18      26
HET    U36  B  19      24
HET    U36  B  20      24
HET    C43  B  21      24
HET    G48  B  22      27
HET    C43  B  23      24
HET    G48  B  24      27
HET     MG  A 100       1
HET     MG  A 106       1
HETNAM     C43 2'-O-METHYOXYETHYL-CYTIDINE-5'-MONOPHOSPHATE
HETNAM     G48 2'-O-METHYOXYETHYL-GUANOSINE-5'-MONOPHOSPHATE
HETNAM     A44 2'-O-METHYOXYETHYL-ADENOSINE 5'-MONOPHOSPHATE
HETNAM     U36 2'-O-METHYOXYETHYL-URIDINE-5'-MONOPHOSPHATE
HETNAM      MG MAGNESIUM ION
FORMUL   1  C43    8(C12 H20 N3 O9 P)
FORMUL   1  G48    8(C13 H20 N5 O9 P)
FORMUL   1  A44    4(C13 H20 N5 O8 P)
FORMUL   1  U36    4(C12 H19 N2 O10 P)
FORMUL   3   MG    2(MG 2+)
FORMUL   5  HOH   *123(H2 O)
LINK        MG    MG A 100                 O   HOH B 104     1555   1555  2.06
LINK        MG    MG A 100                 O   HOH B 103     1555   1555  1.95
LINK        MG    MG A 100                 O   HOH A 101     1555   1555  1.98
LINK        MG    MG A 100                 O   HOH B 102     1555   1555  2.11
LINK        MG    MG A 100                 O   HOH A 105     1555   1555  2.39
LINK        MG    MG A 106                 O   HOH A 108     1555   1555  2.23
LINK         O   HOH A 109                MG    MG A 106     1555   2656  2.00
LINK         O   HOH A 107                MG    MG A 106     1555   2656  1.99
LINK         O3' C43 A   1                 P   G48 A   2     1555   1555  1.61
LINK         O3' G48 A   2                 P   C43 A   3     1555   1555  1.60
LINK         O3' C43 A   3                 P   G48 A   4     1555   1555  1.61
LINK         O3' G48 A   4                 P   A44 A   5     1555   1555  1.59
LINK         O3' A44 A   5                 P   A44 A   6     1555   1555  1.60
LINK         O3' A44 A   6                 P   U36 A   7     1555   1555  1.60
LINK         O3' U36 A   7                 P   U36 A   8     1555   1555  1.59
LINK         O3' U36 A   8                 P   C43 A   9     1555   1555  1.61
LINK         O3' C43 A   9                 P   G48 A  10     1555   1555  1.60
LINK         O3' G48 A  10                 P   C43 A  11     1555   1555  1.59
LINK         O3' C43 A  11                 P   G48 A  12     1555   1555  1.60
LINK         O3' C43 B  13                 P   G48 B  14     1555   1555  1.60
LINK         O3' G48 B  14                 P   C43 B  15     1555   1555  1.61
LINK         O3' C43 B  15                 P   G48 B  16     1555   1555  1.60
LINK         O3' G48 B  16                 P   A44 B  17     1555   1555  1.60
LINK         O3' A44 B  17                 P   A44 B  18     1555   1555  1.60
LINK         O3' A44 B  18                 P   U36 B  19     1555   1555  1.61
LINK         O3' U36 B  19                 P   U36 B  20     1555   1555  1.60
LINK         O3' U36 B  20                 P   C43 B  21     1555   1555  1.61
LINK         O3' C43 B  21                 P   G48 B  22     1555   1555  1.59
LINK         O3' G48 B  22                 P   C43 B  23     1555   1555  1.60
LINK         O3' C43 B  23                 P   G48 B  24     1555   1555  1.59
LINK        MG    MG A 106                 O   HOH A 109     1555   1555  2.04
LINK        MG    MG A 106                 O   HOH A 107     1555   1555  2.02
SITE     1 AC1  5 HOH A 101  HOH A 105  HOH B 102  HOH B 103
SITE     2 AC1  5 HOH B 104
SITE     1 AC2  3 HOH A 107  HOH A 108  HOH A 109
CRYST1   42.000   35.600   47.140  90.00  93.20  90.00 C 1 2 1       8
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.023810  0.000000  0.001331        0.00000
SCALE2      0.000000  0.028090  0.000000        0.00000
SCALE3      0.000000  0.000000  0.021247        0.00000
      
 References