HEADER RNA BINDING PROTEIN/RNA 03-MAY-10 3MUM
TITLE CRYSTAL STRUCTURE OF THE G20A MUTANT C-DI-GMP RIBOSWITH BOUND TO C-DI-
TITLE 2 GMP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A;
COMPND 3 CHAIN: P;
COMPND 4 FRAGMENT: UNP RESIDUES 1-98;
COMPND 5 SYNONYM: U1 SNRNP A, U1-A, U1A;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: G20A MUTANT C-DI-GMP RIBOSWITCH;
COMPND 10 CHAIN: R;
COMPND 11 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: SNRPA;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11;
SOURCE 11 MOL_ID: 2;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 OTHER_DETAILS: PREPARED BY IN VITRO TRANSCRIPTION
KEYWDS RIBOSWITCH, C-DI-GMP, RNA BINDING PROTEIN-RNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR S.A.STROBEL,K.D.SMITH
REVDAT 4 06-SEP-23 3MUM 1 REMARK
REVDAT 3 06-OCT-21 3MUM 1 REMARK SEQADV HETSYN LINK
REVDAT 2 22-SEP-10 3MUM 1 JRNL
REVDAT 1 25-AUG-10 3MUM 0
JRNL AUTH K.D.SMITH,S.V.LIPCHOCK,A.L.LIVINGSTON,C.A.SHANAHAN,
JRNL AUTH 2 S.A.STROBEL
JRNL TITL STRUCTURAL AND BIOCHEMICAL DETERMINANTS OF LIGAND BINDING BY
JRNL TITL 2 THE C-DI-GMP RIBOSWITCH .
JRNL REF BIOCHEMISTRY V. 49 7351 2010
JRNL REFN ISSN 0006-2960
JRNL PMID 20690679
JRNL DOI 10.1021/BI100671E
REMARK 2
REMARK 2 RESOLUTION. 2.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0102
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.73
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2
REMARK 3 NUMBER OF REFLECTIONS : 7514
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 + TEST SET) : 0.211
REMARK 3 R VALUE (WORKING SET) : 0.208
REMARK 3 FREE R VALUE : 0.265
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700
REMARK 3 FREE R VALUE TEST SET COUNT : 372
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98
REMARK 3 REFLECTION IN BIN (WORKING SET) : 461
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.82
REMARK 3 BIN R VALUE (WORKING SET) : 0.3070
REMARK 3 BIN FREE R VALUE SET COUNT : 19
REMARK 3 BIN FREE R VALUE : 0.3820
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 712
REMARK 3 NUCLEIC ACID ATOMS : 1983
REMARK 3 HETEROGEN ATOMS : 48
REMARK 3 SOLVENT ATOMS : 24
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 72.00
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.00
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 OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.481
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.394
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.875
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3007 ; 0.006 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4540 ; 1.070 ; 2.776
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 86 ; 4.806 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 34 ;32.044 ;23.235
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 144 ;16.340 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;22.257 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1518 ; 0.003 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 3MUM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-10.
REMARK 100 THE DEPOSITION ID IS D_1000059013.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 21-AUG-09
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X25
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.1
REMARK 200 MONOCHROMATOR : SI-111 DOUBLE CRYSTAL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7514
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900
REMARK 200 RESOLUTION RANGE LOW (A) : 80.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3
REMARK 200 DATA REDUNDANCY : 6.600
REMARK 200 R MERGE (I) : 0.08200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00
REMARK 200 COMPLETENESS FOR SHELL (%) : 75.2
REMARK 200 DATA REDUNDANCY IN SHELL : 4.80
REMARK 200 R MERGE FOR SHELL (I) : 0.49200
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: PDB ENTRY 3IRW
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.21
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG 550 MME, 5 MM MGSO4, 50 MM
REMARK 280 MES, PH 6.0, 300 MM NACL, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 22.79800
REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3440 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19260 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: P, R
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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET P 1
REMARK 465 ALA P 2
REMARK 465 VAL P 3
REMARK 465 PRO P 4
REMARK 465 GLU P 5
REMARK 465 THR P 6
REMARK 465 ILE P 94
REMARK 465 ALA P 95
REMARK 465 LYS P 96
REMARK 465 MET P 97
REMARK 465 LYS P 98
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 A R 48 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 G R 94 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
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 R 670 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 A R 48 OP2
REMARK 620 2 HOH R 706 O 94.6
REMARK 620 3 HOH R 707 O 85.7 179.7
REMARK 620 4 HOH R 708 O 115.7 90.4 89.6
REMARK 620 5 HOH R 709 O 65.7 89.5 90.5 178.6
REMARK 620 6 HOH R 710 O 154.6 91.2 88.5 89.0 89.6
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG R 671 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH R 711 O
REMARK 620 2 HOH R 712 O 179.7
REMARK 620 3 HOH R 713 O 89.9 90.3
REMARK 620 4 HOH R 714 O 90.1 89.7 180.0
REMARK 620 5 HOH R 715 O 91.1 88.7 89.9 90.1
REMARK 620 6 HOH R 716 O 89.1 91.1 89.3 90.6 179.2
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C2E R 1
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG R 670
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG R 671
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3MUV RELATED DB: PDB
REMARK 900 STRUCTURE OF THE G20A/C92U MUTANT C-DI-GMP RIBOSWITH BOUND TO C-DI-
REMARK 900 AMP
REMARK 900 RELATED ID: 3MUR RELATED DB: PDB
REMARK 900 STRUCTURE OF THE C92U MUTANT C-DI-GMP RIBOSWITH BOUND TO C-DI-GMP
REMARK 900 RELATED ID: 3MUT RELATED DB: PDB
REMARK 900 STRUCTURE OF THE G20A/C92U MUTANT C-DI-GMP RIBOSWITH BOUND TO C-DI-
REMARK 900 GMP
REMARK 900 RELATED ID: 3MXH RELATED DB: PDB
REMARK 900 STRUCTURE OF A C-DI-GMP RIBOSWITCH FROM V. CHOLERAE BOUND TO NATIVE
REMARK 900 METALS
REMARK 900 RELATED ID: 3IRW RELATED DB: PDB
REMARK 900 THE ORIGINAL REPORT OF THE STRUCTURE OF THIS RIBOSWITCH (WILD-TYPE)
DBREF 3MUM P 1 98 UNP P09012 SNRPA_HUMAN 1 98
DBREF 3MUM R 8 98 PDB 3MUM 3MUM 8 98
SEQADV 3MUM HIS P 31 UNP P09012 TYR 31 ENGINEERED MUTATION
SEQADV 3MUM ARG P 36 UNP P09012 GLN 36 ENGINEERED MUTATION
SEQRES 1 P 98 MET ALA VAL PRO GLU THR ARG PRO ASN HIS THR ILE TYR
SEQRES 2 P 98 ILE ASN ASN LEU ASN GLU LYS ILE LYS LYS ASP GLU LEU
SEQRES 3 P 98 LYS LYS SER LEU HIS ALA ILE PHE SER ARG PHE GLY GLN
SEQRES 4 P 98 ILE LEU ASP ILE LEU VAL SER ARG SER LEU LYS MET ARG
SEQRES 5 P 98 GLY GLN ALA PHE VAL ILE PHE LYS GLU VAL SER SER ALA
SEQRES 6 P 98 THR ASN ALA LEU ARG SER MET GLN GLY PHE PRO PHE TYR
SEQRES 7 P 98 ASP LYS PRO MET ARG ILE GLN TYR ALA LYS THR ASP SER
SEQRES 8 P 98 ASP ILE ILE ALA LYS MET LYS
SEQRES 1 R 92 GTP G U C A C G C A C A G A
SEQRES 2 R 92 G C A A A C C A U U C G A
SEQRES 3 R 92 A A G A G U G G G A C G C
SEQRES 4 R 92 A A A G C C U C C G G C C
SEQRES 5 R 92 U A A A C C A U U G C A C
SEQRES 6 R 92 U C C G G U A G G U A G C
SEQRES 7 R 92 G G G G U U A C C G A U G
SEQRES 8 R 92 G
MODRES 3MUM GTP R 8 G GUANOSINE-5'-TRIPHOSPHATE
HET GTP R 8 32
HET C2E R 1 46
HET MG R 670 1
HET MG R 671 1
HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE
HETNAM C2E 9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,
HETNAM 2 C2E 12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,
HETNAM 3 C2E 2-D:3',2'-J][1,3,7,9,2,
HETNAM 4 C2E 8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-
HETNAM 5 C2E 1,9-DIHYDRO-6H-PURIN-6-ONE)
HETNAM MG MAGNESIUM ION
HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE
FORMUL 2 GTP C10 H16 N5 O14 P3
FORMUL 3 C2E C20 H24 N10 O14 P2
FORMUL 4 MG 2(MG 2+)
FORMUL 6 HOH *24(H2 O)
HELIX 1 1 LYS P 22 SER P 35 1 14
HELIX 2 2 SER P 48 ARG P 52 5 5
HELIX 3 3 GLU P 61 SER P 71 1 11
SHEET 1 A 4 ILE P 43 LEU P 44 0
SHEET 2 A 4 GLN P 54 VAL P 57 -1 O PHE P 56 N LEU P 44
SHEET 3 A 4 ILE P 12 ASN P 15 -1 N ILE P 14 O ALA P 55
SHEET 4 A 4 ARG P 83 TYR P 86 -1 O ARG P 83 N ASN P 15
SHEET 1 B 2 PRO P 76 PHE P 77 0
SHEET 2 B 2 LYS P 80 PRO P 81 -1 N LYS P 80 O PHE P 77
LINK O3' GTP R 8 P G R 9 1555 1555 1.60
LINK OP2 A R 48 MG MG R 670 1555 1555 2.79
LINK MG MG R 670 O HOH R 706 1555 1555 2.18
LINK MG MG R 670 O HOH R 707 1555 1555 2.17
LINK MG MG R 670 O HOH R 708 1555 1555 2.18
LINK MG MG R 670 O HOH R 709 1555 1555 2.18
LINK MG MG R 670 O HOH R 710 1555 1555 2.18
LINK MG MG R 671 O HOH R 711 1555 1555 2.18
LINK MG MG R 671 O HOH R 712 1555 1555 2.18
LINK MG MG R 671 O HOH R 713 1555 1555 2.18
LINK MG MG R 671 O HOH R 714 1555 1555 2.18
LINK MG MG R 671 O HOH R 715 1555 1555 2.18
LINK MG MG R 671 O HOH R 716 1555 1555 2.18
SITE 1 AC1 17 G R 14 A R 16 C R 17 A R 18
SITE 2 AC1 17 A R 20 G R 21 C R 46 A R 47
SITE 3 AC1 17 A R 48 A R 49 C R 92 C R 93
SITE 4 AC1 17 MG R 671 HOH R 707 HOH R 711 HOH R 715
SITE 5 AC1 17 HOH R 718
SITE 1 AC2 7 A R 47 A R 48 HOH R 706 HOH R 707
SITE 2 AC2 7 HOH R 708 HOH R 709 HOH R 710
SITE 1 AC3 7 C2E R 1 HOH R 711 HOH R 712 HOH R 713
SITE 2 AC3 7 HOH R 714 HOH R 715 HOH R 716
CRYST1 50.115 45.596 79.821 90.00 93.99 90.00 P 1 21 1 2
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 0.019954 0.000000 0.001392 0.00000
SCALE2 0.000000 0.021932 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012558 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
