HEADER RNA BINDING PROTEIN/RNA 07-MAY-10 3MXH
TITLE NATIVE STRUCTURE OF A C-DI-GMP RIBOSWITCH FROM V. CHOLERAE
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: 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: IN VITRO TRANSCRIBED FROM LINEAR DNA
KEYWDS RNA, RIBOSWITCH, C-DI-GMP, RNA BINDING PROTEIN-RNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR S.A.STROBEL,K.D.SMITH
REVDAT 3 06-SEP-23 3MXH 1 REMARK SEQADV HETSYN LINK
REVDAT 2 22-SEP-10 3MXH 1 JRNL
REVDAT 1 25-AUG-10 3MXH 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. 2.30 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) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.34
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7
REMARK 3 NUMBER OF REFLECTIONS : 15201
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) : 0.203
REMARK 3 R VALUE (WORKING SET) : 0.202
REMARK 3 FREE R VALUE : 0.239
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 816
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) : 2.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1019
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.66
REMARK 3 BIN R VALUE (WORKING SET) : 0.4650
REMARK 3 BIN FREE R VALUE SET COUNT : 49
REMARK 3 BIN FREE R VALUE : 0.4130
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 712
REMARK 3 NUCLEIC ACID ATOMS : 1984
REMARK 3 HETEROGEN ATOMS : 51
REMARK 3 SOLVENT ATOMS : 169
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 62.40
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.32
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.92000
REMARK 3 B22 (A**2) : -0.50000
REMARK 3 B33 (A**2) : -1.98000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 3.33000
REMARK 3 B23 (A**2) : 0.00000
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): 0.247
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.204
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.433
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3020 ; 0.006 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4567 ; 0.936 ; 2.777
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 86 ; 5.313 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 34 ;37.972 ;23.235
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 144 ;14.270 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;17.356 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 573 ; 0.046 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1519 ; 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): 434 ; 0.918 ; 5.000
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 703 ; 1.576 ;10.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2586 ; 1.382 ; 5.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3863 ; 2.122 ;10.000
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 : 5
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : R 8 R 20
REMARK 3 ORIGIN FOR THE GROUP (A): -14.2399 -4.3803 22.3020
REMARK 3 T TENSOR
REMARK 3 T11: 0.4632 T22: 0.2931
REMARK 3 T33: 0.1569 T12: 0.0199
REMARK 3 T13: 0.1601 T23: 0.0195
REMARK 3 L TENSOR
REMARK 3 L11: 17.1276 L22: 7.0041
REMARK 3 L33: 7.0560 L12: 2.5107
REMARK 3 L13: 1.1895 L23: -1.9606
REMARK 3 S TENSOR
REMARK 3 S11: 0.1639 S12: -0.8546 S13: -0.5377
REMARK 3 S21: 0.8490 S22: -0.1776 S23: 0.4128
REMARK 3 S31: 0.0910 S32: -0.3856 S33: 0.0137
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : R 21 R 65
REMARK 3 ORIGIN FOR THE GROUP (A): -2.2192 -1.7566 -6.0709
REMARK 3 T TENSOR
REMARK 3 T11: 0.2817 T22: 0.1041
REMARK 3 T33: 0.1784 T12: 0.0457
REMARK 3 T13: -0.0720 T23: 0.0279
REMARK 3 L TENSOR
REMARK 3 L11: 2.2231 L22: 2.5465
REMARK 3 L33: 2.2971 L12: 0.7402
REMARK 3 L13: -1.4779 L23: -0.0342
REMARK 3 S TENSOR
REMARK 3 S11: -0.0468 S12: 0.4048 S13: -0.0374
REMARK 3 S21: -0.4174 S22: 0.0628 S23: 0.1106
REMARK 3 S31: -0.0508 S32: -0.2331 S33: -0.0160
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : R 75 R 98
REMARK 3 ORIGIN FOR THE GROUP (A): -15.0206 -4.0060 2.9990
REMARK 3 T TENSOR
REMARK 3 T11: 0.2549 T22: 0.2456
REMARK 3 T33: 0.3190 T12: 0.0814
REMARK 3 T13: 0.0189 T23: 0.0222
REMARK 3 L TENSOR
REMARK 3 L11: 2.0878 L22: 2.3987
REMARK 3 L33: 5.0541 L12: 0.7014
REMARK 3 L13: 0.6373 L23: -0.4760
REMARK 3 S TENSOR
REMARK 3 S11: -0.0147 S12: 0.2956 S13: 0.0208
REMARK 3 S21: -0.1695 S22: 0.0196 S23: 0.3893
REMARK 3 S31: -0.3833 S32: -0.6250 S33: -0.0049
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : R 660 R 669
REMARK 3 ORIGIN FOR THE GROUP (A): -17.7168 10.0842 -32.7336
REMARK 3 T TENSOR
REMARK 3 T11: 0.3427 T22: 0.5249
REMARK 3 T33: 1.1319 T12: 0.0481
REMARK 3 T13: -0.0876 T23: -0.0748
REMARK 3 L TENSOR
REMARK 3 L11: 9.2811 L22: 3.3611
REMARK 3 L33: 5.4248 L12: 2.4823
REMARK 3 L13: -3.6152 L23: -4.2577
REMARK 3 S TENSOR
REMARK 3 S11: 0.9414 S12: -0.0554 S13: 1.7623
REMARK 3 S21: 0.2947 S22: 0.4019 S23: 1.1096
REMARK 3 S31: -0.4251 S32: -0.3753 S33: -1.3432
REMARK 3
REMARK 3 TLS GROUP : 5
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : P 7 P 93
REMARK 3 ORIGIN FOR THE GROUP (A): -7.0168 16.3283 -40.3012
REMARK 3 T TENSOR
REMARK 3 T11: 0.2482 T22: 0.3578
REMARK 3 T33: 0.7960 T12: 0.0520
REMARK 3 T13: -0.0008 T23: 0.0215
REMARK 3 L TENSOR
REMARK 3 L11: 8.5598 L22: 26.6322
REMARK 3 L33: 10.8829 L12: 1.6941
REMARK 3 L13: -1.4201 L23: -7.7860
REMARK 3 S TENSOR
REMARK 3 S11: 0.5642 S12: 0.5106 S13: 1.8324
REMARK 3 S21: -0.9445 S22: -0.0686 S23: 0.4835
REMARK 3 S31: -0.6197 S32: 0.2963 S33: -0.4956
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 3MXH 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_1000059116.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 26-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 : X29A
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 : SAGITALLY FOCUSED SI(111)
REMARK 200 OPTICS : VERTICALLY FOCUSING MIRROR
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 : 15201
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
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 (%) : 97.4
REMARK 200 DATA REDUNDANCY : 5.300
REMARK 200 R MERGE (I) : 0.07300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40
REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9
REMARK 200 DATA REDUNDANCY IN SHELL : 4.40
REMARK 200 R MERGE FOR SHELL (I) : 0.52800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100
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 (%): 44.71
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG550MME, 50 MM MES, PH 6.0, 5 MM
REMARK 280 MGSO4, 300 MM NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE
REMARK 280 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 22.82600
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: 3810 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19250 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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. = 6.2 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 THR P 89 115.32 -165.90
REMARK 500 SER P 91 -91.60 -77.07
REMARK 500 ASP P 92 -126.61 42.63
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 P 99 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH P 109 O
REMARK 620 2 HOH P 110 O 179.9
REMARK 620 3 HOH P 111 O 89.9 89.9
REMARK 620 4 HOH P 112 O 90.0 90.1 179.8
REMARK 620 5 HOH P 113 O 90.0 90.0 90.0 90.2
REMARK 620 6 HOH P 114 O 90.1 89.9 90.1 89.7 179.9
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG R 2 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH R 734 O
REMARK 620 2 HOH R 735 O 179.7
REMARK 620 3 HOH R 736 O 89.9 90.4
REMARK 620 4 HOH R 737 O 90.0 89.7 179.7
REMARK 620 5 HOH R 738 O 89.9 90.1 90.1 90.1
REMARK 620 6 HOH R 739 O 90.5 89.6 89.7 90.0 179.6
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG R 4 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH R 100 O
REMARK 620 2 HOH R 161 O 67.9
REMARK 620 N 1
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG R 5 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 G R 42 O6
REMARK 620 2 HOH R 740 O 83.8
REMARK 620 3 HOH R 741 O 96.2 179.8
REMARK 620 4 HOH R 742 O 82.7 90.4 89.8
REMARK 620 5 HOH R 743 O 96.5 89.5 90.4 179.3
REMARK 620 6 HOH R 744 O 170.1 90.0 90.0 89.6 91.2
REMARK 620 N 1 2 3 4 5
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 729 O 158.8
REMARK 620 3 HOH R 730 O 110.5 90.4
REMARK 620 4 HOH R 731 O 69.9 89.1 179.5
REMARK 620 5 HOH R 732 O 88.0 88.9 89.5 90.4
REMARK 620 6 HOH R 733 O 92.6 90.6 90.3 89.8 179.4
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 MG P 99
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C2E R 1
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG R 670
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG R 2
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG R 4
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG R 5
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3MUM RELATED DB: PDB
REMARK 900 STRUCTURE OF THE G20A MUTANT C-DI-GMP RIBOSWITH BOUND TO C-DI-GMP
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: 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: 3IRW RELATED DB: PDB
REMARK 900 THE ORIGINAL REPORT OF THE STRUCTURE OF THIS RIBOSWITCH (WILD-TYPE)
DBREF 3MXH P 1 98 UNP P09012 SNRPA_HUMAN 1 98
DBREF 3MXH R 8 98 PDB 3MXH 3MXH 8 98
SEQADV 3MXH HIS P 31 UNP P09012 TYR 31 ENGINEERED MUTATION
SEQADV 3MXH 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 G
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 3MXH GTP R 8 G GUANOSINE-5'-TRIPHOSPHATE
HET GTP R 8 32
HET MG P 99 1
HET C2E R 1 46
HET MG R 670 1
HET MG R 2 1
HET MG R 4 1
HET MG R 5 1
HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE
HETNAM MG MAGNESIUM ION
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)
HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE
FORMUL 2 GTP C10 H16 N5 O14 P3
FORMUL 3 MG 5(MG 2+)
FORMUL 4 C2E C20 H24 N10 O14 P2
FORMUL 9 HOH *169(H2 O)
HELIX 1 1 LYS P 22 SER P 35 1 14
HELIX 2 2 GLU P 61 MET P 72 1 12
SHEET 1 A 4 ILE P 40 LEU P 44 0
SHEET 2 A 4 ALA P 55 PHE P 59 -1 O ILE P 58 N LEU P 41
SHEET 3 A 4 THR P 11 ASN P 15 -1 N ILE P 14 O ALA P 55
SHEET 4 A 4 ARG P 83 TYR P 86 -1 O GLN P 85 N TYR P 13
SHEET 1 B 2 PRO P 76 PHE P 77 0
SHEET 2 B 2 LYS P 80 PRO P 81 -1 O LYS P 80 N PHE P 77
LINK O3' GTP R 8 P G R 9 1555 1555 1.61
LINK MG MG P 99 O HOH P 109 1555 1555 2.18
LINK MG MG P 99 O HOH P 110 1555 1555 2.18
LINK MG MG P 99 O HOH P 111 1555 1555 2.18
LINK MG MG P 99 O HOH P 112 1555 1555 2.18
LINK MG MG P 99 O HOH P 113 1555 1555 2.18
LINK MG MG P 99 O HOH P 114 1555 1555 2.18
LINK MG MG R 2 O HOH R 734 1555 1555 2.19
LINK MG MG R 2 O HOH R 735 1555 1555 2.18
LINK MG MG R 2 O HOH R 736 1555 1555 2.18
LINK MG MG R 2 O HOH R 737 1555 1555 2.18
LINK MG MG R 2 O HOH R 738 1555 1555 2.18
LINK MG MG R 2 O HOH R 739 1555 1555 2.17
LINK MG MG R 4 O HOH R 100 1555 1555 2.21
LINK MG MG R 4 O HOH R 161 1555 1555 2.42
LINK MG MG R 5 O6 G R 42 1555 1555 2.40
LINK MG MG R 5 O HOH R 740 1555 1555 2.18
LINK MG MG R 5 O HOH R 741 1555 1555 2.18
LINK MG MG R 5 O HOH R 742 1555 1555 2.18
LINK MG MG R 5 O HOH R 743 1555 1555 2.18
LINK MG MG R 5 O HOH R 744 1555 1555 2.18
LINK OP2 A R 48 MG MG R 670 1555 1555 2.18
LINK MG MG R 670 O HOH R 729 1555 1555 2.18
LINK MG MG R 670 O HOH R 730 1555 1555 2.18
LINK MG MG R 670 O HOH R 731 1555 1555 2.18
LINK MG MG R 670 O HOH R 732 1555 1555 2.18
LINK MG MG R 670 O HOH R 733 1555 1555 2.18
SITE 1 AC1 7 ARG P 70 HOH P 109 HOH P 110 HOH P 111
SITE 2 AC1 7 HOH P 112 HOH P 113 HOH P 114
SITE 1 AC2 23 MG R 2 G R 14 A R 16 C R 17
SITE 2 AC2 23 A R 18 G R 20 G R 21 C R 46
SITE 3 AC2 23 A R 47 A R 48 A R 49 C R 92
SITE 4 AC2 23 C R 93 HOH R 140 HOH R 671 HOH R 673
SITE 5 AC2 23 HOH R 676 HOH R 687 HOH R 717 HOH R 732
SITE 6 AC2 23 HOH R 734 HOH R 736 HOH R 738
SITE 1 AC3 7 A R 47 A R 48 HOH R 729 HOH R 730
SITE 2 AC3 7 HOH R 731 HOH R 732 HOH R 733
SITE 1 AC4 7 C2E R 1 HOH R 734 HOH R 735 HOH R 736
SITE 2 AC4 7 HOH R 737 HOH R 738 HOH R 739
SITE 1 AC5 4 HOH R 70 U R 81 HOH R 100 HOH R 161
SITE 1 AC6 6 G R 42 HOH R 740 HOH R 741 HOH R 742
SITE 2 AC6 6 HOH R 743 HOH R 744
CRYST1 50.243 45.652 80.248 90.00 93.74 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 0.019903 0.000000 0.001300 0.00000
SCALE2 0.000000 0.021905 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012488 0.00000
(ATOM LINES ARE NOT SHOWN.)
END