HEADER RNA/RNA BINDING PROTEIN 26-NOV-09 3KTV TITLE CRYSTAL STRUCTURE OF THE HUMAN SRP19/S-DOMAIN SRP RNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: SRP RNA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: S DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN; COMPND 8 CHAIN: B, D; COMPND 9 SYNONYM: SRP19; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: SRP RNA; COMPND 13 CHAIN: C; COMPND 14 FRAGMENT: S DOMAIN; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5ALPHA; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PUC19; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: SRP19; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PET21D; SOURCE 20 MOL_ID: 3; SOURCE 21 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 22 ORGANISM_COMMON: HUMAN; SOURCE 23 ORGANISM_TAXID: 9606; SOURCE 24 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 25 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 26 EXPRESSION_SYSTEM_STRAIN: DH5ALPHA; SOURCE 27 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 28 EXPRESSION_SYSTEM_PLASMID: PUC19 KEYWDS RIBONUCLEOPROTEIN COMPLEX, RNA-RNA TERTIARY INTERACTIONS, ASYMMETRIC KEYWDS 2 LOOP, RNA-BINDING, SIGNAL RECOGNITION PARTICLE, RNA-RNA BINDING KEYWDS 3 PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.WILD,G.BANGE,G.BOZKURT,I.SINNING REVDAT 4 06-SEP-23 3KTV 1 REMARK SEQADV LINK REVDAT 3 06-JUL-11 3KTV 1 JRNL REVDAT 2 23-FEB-10 3KTV 1 JRNL REVDAT 1 16-FEB-10 3KTV 0 JRNL AUTH K.WILD,G.BANGE,G.BOZKURT,B.SEGNITZ,A.HENDRICKS,I.SINNING JRNL TITL STRUCTURAL INSIGHTS INTO THE ASSEMBLY OF THE HUMAN AND JRNL TITL 2 ARCHAEAL SIGNAL RECOGNITION PARTICLES. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 66 295 2010 JRNL REFN ISSN 0907-4449 JRNL PMID 20179341 JRNL DOI 10.1107/S0907444910000879 REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 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) : 3.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 14727 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) : 0.293 REMARK 3 R VALUE (WORKING SET) : 0.291 REMARK 3 FREE R VALUE : 0.329 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 711 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) : 3.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 969 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.3840 REMARK 3 BIN FREE R VALUE SET COUNT : 47 REMARK 3 BIN FREE R VALUE : 0.4970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1725 REMARK 3 NUCLEIC ACID ATOMS : 4659 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 88.01 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): 0.872 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.804 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 : 0.879 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6970 ; 0.007 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10502 ; 1.352 ; 2.769 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 212 ; 5.666 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 84 ;34.193 ;23.571 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 331 ;17.281 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;12.058 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3594 ; 0.004 ; 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 : NONE REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 3KTV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056440. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87260 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14852 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.800 REMARK 200 RESOLUTION RANGE LOW (A) : 70.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10300 REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.60800 REMARK 200 FOR SHELL : 1.300 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 1LNG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NAOAC, 0.75 M KF, 2.2 M REMARK 280 (NH4)2SO4, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 146.65000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.06000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.06000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 219.97500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.06000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.06000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 73.32500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.06000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.06000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 219.97500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.06000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.06000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 73.32500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 146.65000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 2470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 2 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: 2460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 B 1 REMARK 465 ALA B 2 REMARK 465 CYS B 3 REMARK 465 ALA B 4 REMARK 465 ALA B 5 REMARK 465 ALA B 6 REMARK 465 ARG B 7 REMARK 465 SER B 8 REMARK 465 PRO B 9 REMARK 465 LYS B 116 REMARK 465 THR B 117 REMARK 465 ARG B 118 REMARK 465 THR B 119 REMARK 465 GLN B 120 REMARK 465 LEU B 121 REMARK 465 GLU B 122 REMARK 465 HIS B 123 REMARK 465 HIS B 124 REMARK 465 HIS B 125 REMARK 465 HIS B 126 REMARK 465 HIS B 127 REMARK 465 HIS B 128 REMARK 465 MET D 1 REMARK 465 ALA D 2 REMARK 465 CYS D 3 REMARK 465 ALA D 4 REMARK 465 ALA D 5 REMARK 465 ALA D 6 REMARK 465 ARG D 7 REMARK 465 LYS D 116 REMARK 465 THR D 117 REMARK 465 ARG D 118 REMARK 465 THR D 119 REMARK 465 GLN D 120 REMARK 465 LEU D 121 REMARK 465 GLU D 122 REMARK 465 HIS D 123 REMARK 465 HIS D 124 REMARK 465 HIS D 125 REMARK 465 HIS D 126 REMARK 465 HIS D 127 REMARK 465 HIS D 128 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CB SER D 8 OE1 GLU D 89 1.09 REMARK 500 N6 A C 172 N6 A C 173 1.32 REMARK 500 C2 G A 227 O4 U A 228 1.38 REMARK 500 O2' A C 183 OP1 A C 184 1.47 REMARK 500 OG SER D 8 OE1 GLU D 89 1.52 REMARK 500 N7 G C 164 C8 A C 176 1.57 REMARK 500 N4 C A 126 O6 G A 224 1.60 REMARK 500 O4' U A 128 N1 A A 173 1.62 REMARK 500 O2 U A 226 C8 G A 227 1.63 REMARK 500 O2' C A 185 O5' C A 186 1.64 REMARK 500 O2' A C 173 O2' U C 223 1.65 REMARK 500 N2 G A 227 O4 U A 228 1.66 REMARK 500 N7 A C 172 C5 A C 173 1.67 REMARK 500 C2 A A 127 C6 U A 128 1.71 REMARK 500 C2 A A 183 OP2 C A 186 1.71 REMARK 500 O2' A A 184 OP1 C A 185 1.71 REMARK 500 O2' G C 168 OP1 C C 169 1.73 REMARK 500 O2' C A 161 O2' A A 214 1.73 REMARK 500 C2 A C 183 OP2 C C 186 1.74 REMARK 500 C6 A C 172 N6 A C 173 1.75 REMARK 500 N3 G A 227 O4 U A 228 1.75 REMARK 500 N2 G A 177 C4 G A 178 1.76 REMARK 500 NZ LYS B 64 N ASN B 65 1.76 REMARK 500 O GLN D 88 N GLY D 91 1.77 REMARK 500 C5' G A 122 OP1 C A 123 1.80 REMARK 500 N2 G A 224 C2 C A 225 1.80 REMARK 500 O2' C A 169 OP2 U A 171 1.83 REMARK 500 N2 G A 198 C4 C A 202 1.84 REMARK 500 O2' A C 172 O2' G C 224 1.84 REMARK 500 CB SER D 8 CD GLU D 89 1.84 REMARK 500 N1 A A 183 OP2 C A 186 1.86 REMARK 500 C2' C A 169 OP1 U A 171 1.90 REMARK 500 OP2 G C 164 C8 A C 176 1.91 REMARK 500 C1' A C 172 O2' G C 224 1.91 REMARK 500 C1' U A 128 N1 A A 173 1.93 REMARK 500 C2' A C 172 O2' G C 224 1.93 REMARK 500 O SER D 100 OG SER D 103 1.95 REMARK 500 O VAL D 76 N TYR D 78 1.95 REMARK 500 O ILE D 112 N LYS D 114 1.95 REMARK 500 O GLN B 88 N ASP B 90 1.97 REMARK 500 N7 G C 164 N7 A C 176 1.97 REMARK 500 OD1 ASN B 73 N ASP B 75 1.98 REMARK 500 O5' C A 129 O2' G A 174 1.99 REMARK 500 O2' C A 169 P U A 171 1.99 REMARK 500 O PHE D 15 NH2 ARG D 83 2.00 REMARK 500 O2' A C 172 O3' G C 224 2.00 REMARK 500 OP1 G C 148 NH2 ARG D 14 2.00 REMARK 500 O2 C A 145 N2 G A 152 2.01 REMARK 500 C2 U A 171 C5' A A 173 2.01 REMARK 500 C1' C A 169 OP1 U A 171 2.01 REMARK 500 REMARK 500 THIS ENTRY HAS 75 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 N3 C A 185 N3 C A 185 7555 1.65 REMARK 500 N4 C A 185 N4 C A 185 7555 1.72 REMARK 500 O3' C A 220 O2' C C 123 3454 1.83 REMARK 500 O2 C A 185 O2 C A 185 7555 1.87 REMARK 500 C2 A C 184 O2' A C 205 7555 1.99 REMARK 500 REMARK 500 REMARK: NULL 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 U A 128 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 G A 165 C3' - C2' - C1' ANGL. DEV. = -4.3 DEGREES REMARK 500 G A 180 O5' - C5' - C4' ANGL. DEV. = -5.9 DEGREES REMARK 500 C A 185 C3' - O3' - P ANGL. DEV. = -9.3 DEGREES REMARK 500 A A 201 C3' - O3' - P ANGL. DEV. = -8.0 DEGREES REMARK 500 A A 215 C3' - O3' - P ANGL. DEV. = -7.7 DEGREES REMARK 500 C C 123 O5' - C5' - C4' ANGL. DEV. = -6.9 DEGREES REMARK 500 G C 138 C4' - C3' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 C C 143 O4' - C1' - N1 ANGL. DEV. = -4.9 DEGREES REMARK 500 A C 184 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 C C 185 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 G C 198 C4' - C3' - C2' ANGL. DEV. = -6.9 DEGREES REMARK 500 A C 200 C8 - N9 - C4 ANGL. DEV. = 2.5 DEGREES REMARK 500 G C 224 O5' - C5' - C4' ANGL. DEV. = -4.9 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 ASP B 13 -8.00 -55.60 REMARK 500 ALA B 40 171.73 -51.58 REMARK 500 ALA B 55 37.56 -79.78 REMARK 500 GLU B 63 57.95 -102.80 REMARK 500 LYS B 64 -13.49 -32.00 REMARK 500 LYS B 66 170.32 -47.20 REMARK 500 ARG B 70 39.55 -65.34 REMARK 500 GLN B 77 -31.49 -29.93 REMARK 500 LEU B 86 -76.84 -91.37 REMARK 500 GLU B 89 -47.35 -9.58 REMARK 500 VAL B 96 -30.00 -28.84 REMARK 500 PRO B 113 -6.81 -55.01 REMARK 500 PHE D 15 138.67 -21.83 REMARK 500 ILE D 37 -51.32 -29.99 REMARK 500 ASN D 43 52.74 73.56 REMARK 500 ALA D 55 42.50 -62.36 REMARK 500 VAL D 56 7.61 -158.34 REMARK 500 LYS D 64 -37.42 -24.41 REMARK 500 LYS D 66 154.34 -45.00 REMARK 500 ARG D 70 20.10 -68.75 REMARK 500 GLU D 71 67.26 -107.09 REMARK 500 VAL D 76 -74.01 -40.44 REMARK 500 GLN D 77 -24.03 -27.49 REMARK 500 GLU D 89 -38.18 -20.74 REMARK 500 VAL D 96 -32.97 -18.50 REMARK 500 PHE D 98 69.93 -117.77 REMARK 500 PRO D 113 -7.60 -45.20 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 C 4 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G C 193 O3' REMARK 620 2 G C 193 O5' 79.6 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K D 129 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KTW RELATED DB: PDB DBREF1 3KTV A 123 227 GB NR_002715 DBREF2 3KTV A NR_002715.1 123 227 DBREF 3KTV B 1 120 UNP P09132 SRP19_HUMAN 1 120 DBREF1 3KTV C 123 227 GB NR_002715 DBREF2 3KTV C NR_002715.1 123 227 DBREF 3KTV D 1 120 UNP P09132 SRP19_HUMAN 1 120 SEQADV 3KTV G A 122 GB NR_002715 INSERTION SEQADV 3KTV U A 228 GB NR_002715 INSERTION SEQADV 3KTV A A 229 GB NR_002715 INSERTION SEQADV 3KTV LEU B 121 UNP P09132 EXPRESSION TAG SEQADV 3KTV GLU B 122 UNP P09132 EXPRESSION TAG SEQADV 3KTV HIS B 123 UNP P09132 EXPRESSION TAG SEQADV 3KTV HIS B 124 UNP P09132 EXPRESSION TAG SEQADV 3KTV HIS B 125 UNP P09132 EXPRESSION TAG SEQADV 3KTV HIS B 126 UNP P09132 EXPRESSION TAG SEQADV 3KTV HIS B 127 UNP P09132 EXPRESSION TAG SEQADV 3KTV HIS B 128 UNP P09132 EXPRESSION TAG SEQADV 3KTV GDP C 122 GB NR_002715 INSERTION SEQADV 3KTV U C 228 GB NR_002715 INSERTION SEQADV 3KTV A C 229 GB NR_002715 INSERTION SEQADV 3KTV LEU D 121 UNP P09132 EXPRESSION TAG SEQADV 3KTV GLU D 122 UNP P09132 EXPRESSION TAG SEQADV 3KTV HIS D 123 UNP P09132 EXPRESSION TAG SEQADV 3KTV HIS D 124 UNP P09132 EXPRESSION TAG SEQADV 3KTV HIS D 125 UNP P09132 EXPRESSION TAG SEQADV 3KTV HIS D 126 UNP P09132 EXPRESSION TAG SEQADV 3KTV HIS D 127 UNP P09132 EXPRESSION TAG SEQADV 3KTV HIS D 128 UNP P09132 EXPRESSION TAG SEQRES 1 A 108 G C G G C A U C A A U A U SEQRES 2 A 108 G G U G A C C U C C C G G SEQRES 3 A 108 G A G C G G G G G A C C A SEQRES 4 A 108 C C A G G U U G C C U A A SEQRES 5 A 108 G G A G G G G U G A A C C SEQRES 6 A 108 G G C C C A G G U C G G A SEQRES 7 A 108 A A C G G A G C A G G U C SEQRES 8 A 108 A A A A C U C C C G U G C SEQRES 9 A 108 U G U A SEQRES 1 B 128 MET ALA CYS ALA ALA ALA ARG SER PRO ALA ASP GLN ASP SEQRES 2 B 128 ARG PHE ILE CYS ILE TYR PRO ALA TYR LEU ASN ASN LYS SEQRES 3 B 128 LYS THR ILE ALA GLU GLY ARG ARG ILE PRO ILE SER LYS SEQRES 4 B 128 ALA VAL GLU ASN PRO THR ALA THR GLU ILE GLN ASP VAL SEQRES 5 B 128 CYS SER ALA VAL GLY LEU ASN VAL PHE LEU GLU LYS ASN SEQRES 6 B 128 LYS MET TYR SER ARG GLU TRP ASN ARG ASP VAL GLN TYR SEQRES 7 B 128 ARG GLY ARG VAL ARG VAL GLN LEU LYS GLN GLU ASP GLY SEQRES 8 B 128 SER LEU CYS LEU VAL GLN PHE PRO SER ARG LYS SER VAL SEQRES 9 B 128 MET LEU TYR ALA ALA GLU MET ILE PRO LYS LEU LYS THR SEQRES 10 B 128 ARG THR GLN LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 C 108 GDP C G G C A U C A A U A U SEQRES 2 C 108 G G U G A C C U C C C G G SEQRES 3 C 108 G A G C G G G G G A C C A SEQRES 4 C 108 C C A G G U U G C C U A A SEQRES 5 C 108 G G A G G G G U G A A C C SEQRES 6 C 108 G G C C C A G G U C G G A SEQRES 7 C 108 A A C G G A G C A G G U C SEQRES 8 C 108 A A A A C U C C C G U G C SEQRES 9 C 108 U G U A SEQRES 1 D 128 MET ALA CYS ALA ALA ALA ARG SER PRO ALA ASP GLN ASP SEQRES 2 D 128 ARG PHE ILE CYS ILE TYR PRO ALA TYR LEU ASN ASN LYS SEQRES 3 D 128 LYS THR ILE ALA GLU GLY ARG ARG ILE PRO ILE SER LYS SEQRES 4 D 128 ALA VAL GLU ASN PRO THR ALA THR GLU ILE GLN ASP VAL SEQRES 5 D 128 CYS SER ALA VAL GLY LEU ASN VAL PHE LEU GLU LYS ASN SEQRES 6 D 128 LYS MET TYR SER ARG GLU TRP ASN ARG ASP VAL GLN TYR SEQRES 7 D 128 ARG GLY ARG VAL ARG VAL GLN LEU LYS GLN GLU ASP GLY SEQRES 8 D 128 SER LEU CYS LEU VAL GLN PHE PRO SER ARG LYS SER VAL SEQRES 9 D 128 MET LEU TYR ALA ALA GLU MET ILE PRO LYS LEU LYS THR SEQRES 10 D 128 ARG THR GLN LEU GLU HIS HIS HIS HIS HIS HIS MODRES 3KTV GDP C 122 G GUANOSINE-5'-DIPHOSPHATE HET GDP C 122 28 HET K A 1 1 HET MG A 6 1 HET K C 2 1 HET MG C 4 1 HET MG C 5 1 HET K D 129 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM K POTASSIUM ION HETNAM MG MAGNESIUM ION FORMUL 3 GDP C10 H15 N5 O11 P2 FORMUL 5 K 3(K 1+) FORMUL 6 MG 3(MG 2+) HELIX 1 1 ASP B 11 PHE B 15 5 5 HELIX 2 2 TYR B 19 ASN B 24 5 6 HELIX 3 3 THR B 45 ALA B 55 1 11 HELIX 4 4 ASP B 75 ARG B 79 5 5 HELIX 5 5 SER B 100 ILE B 112 1 13 HELIX 6 6 TYR D 19 ASN D 24 5 6 HELIX 7 7 PRO D 36 ALA D 40 5 5 HELIX 8 8 THR D 45 ALA D 55 1 11 HELIX 9 9 ASP D 75 ARG D 79 5 5 HELIX 10 10 SER D 100 ILE D 112 1 13 HELIX 11 11 PRO D 113 LEU D 115 5 3 SHEET 1 A 3 ILE B 16 ILE B 18 0 SHEET 2 A 3 VAL B 82 GLN B 85 -1 O VAL B 82 N ILE B 18 SHEET 3 A 3 ASN B 59 LEU B 62 -1 N PHE B 61 O ARG B 83 SHEET 1 B 2 LYS B 87 GLN B 88 0 SHEET 2 B 2 SER B 92 LEU B 93 -1 O SER B 92 N GLN B 88 SHEET 1 C 3 ILE D 16 ILE D 18 0 SHEET 2 C 3 VAL D 82 GLN D 85 -1 O VAL D 84 N ILE D 16 SHEET 3 C 3 ASN D 59 LEU D 62 -1 N ASN D 59 O GLN D 85 SHEET 1 D 2 LYS D 87 GLN D 88 0 SHEET 2 D 2 SER D 92 LEU D 93 -1 O SER D 92 N GLN D 88 LINK MG MG A 6 O6 G A 155 1555 1555 2.88 LINK MG MG C 4 O3' G C 193 1555 1555 2.38 LINK MG MG C 4 O5' G C 193 1555 1555 2.81 LINK OE1 GLN D 88 K K D 129 1555 1555 3.40 SITE 1 AC1 3 ASN D 59 GLN D 88 CYS D 94 SITE 1 AC2 2 G C 193 G C 194 SITE 1 AC3 1 A C 139 SITE 1 AC4 2 G A 155 G A 156 CRYST1 100.120 100.120 293.300 90.00 90.00 90.00 P 43 21 2 16 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 0.009988 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009988 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003409 0.00000