HEADER CHAPERONE 13-JAN-21 7DVC TITLE CRYSTAL STRUCTURE OF THE COMPUTATIONALLY DESIGNED REDPBB_SYM1 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: REDPBB_SYM1 PROTEIN; COMPND 3 CHAIN: A, C, E, F, B, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DOUBLE PSI BETA BARREL, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR S.YAGI,S.TAGAMI,A.K.PADHI,K.Y.J.ZHANG REVDAT 3 03-APR-24 7DVC 1 REMARK REVDAT 2 17-NOV-21 7DVC 1 JRNL REVDAT 1 29-SEP-21 7DVC 0 JRNL AUTH S.YAGI,A.K.PADHI,J.VUCINIC,S.BARBE,T.SCHIEX,R.NAKAGAWA, JRNL AUTH 2 D.SIMONCINI,K.Y.J.ZHANG,S.TAGAMI JRNL TITL SEVEN AMINO ACID TYPES SUFFICE TO CREATE THE CORE FOLD OF JRNL TITL 2 RNA POLYMERASE. JRNL REF J.AM.CHEM.SOC. V. 143 15998 2021 JRNL REFN ESSN 1520-5126 JRNL PMID 34559526 JRNL DOI 10.1021/JACS.1C05367 REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.490 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 94530 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.2980 - 4.1073 1.00 7051 152 0.1673 0.1777 REMARK 3 2 4.1073 - 3.2603 1.00 6779 146 0.1353 0.1561 REMARK 3 3 3.2603 - 2.8483 1.00 6695 145 0.1579 0.1655 REMARK 3 4 2.8483 - 2.5879 1.00 6642 144 0.1622 0.1697 REMARK 3 5 2.5879 - 2.4024 1.00 6637 143 0.1676 0.1660 REMARK 3 6 2.4024 - 2.2608 1.00 6618 143 0.1673 0.1808 REMARK 3 7 2.2608 - 2.1475 1.00 6606 142 0.1682 0.1844 REMARK 3 8 2.1475 - 2.0540 1.00 6564 143 0.1689 0.1962 REMARK 3 9 2.0540 - 1.9750 1.00 6570 141 0.1776 0.1815 REMARK 3 10 1.9750 - 1.9068 1.00 6569 143 0.1744 0.1842 REMARK 3 11 1.9068 - 1.8472 1.00 6516 140 0.1893 0.1924 REMARK 3 12 1.8472 - 1.7944 1.00 6571 143 0.2018 0.2124 REMARK 3 13 1.7944 - 1.7472 1.00 6540 141 0.2248 0.2263 REMARK 3 14 1.7472 - 1.7050 0.95 6173 133 0.2596 0.2695 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.99 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7DVC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1300020169. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 94555 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 28.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: COMPUTATIONALLY DESIGNED MODE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM ACETATE PH3.8, 2M NACL, REMARK 280 400 MM LITHIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 88.66200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 49.07550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.07550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 132.99300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.07550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 49.07550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 44.33100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 49.07550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.07550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 132.99300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 49.07550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.07550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 44.33100 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 88.66200 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: F 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: 5 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 6 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 O HOH F 263 O HOH F 271 1.09 REMARK 500 O HOH A 212 O HOH A 216 1.12 REMARK 500 O HOH A 305 O HOH A 316 1.17 REMARK 500 O HOH C 214 O HOH C 281 1.25 REMARK 500 O HOH E 246 O HOH E 274 1.29 REMARK 500 O HOH C 212 O HOH F 215 1.29 REMARK 500 O HOH B 290 O HOH B 310 1.32 REMARK 500 O HOH E 287 O HOH E 290 1.34 REMARK 500 O HOH C 208 O HOH C 289 1.35 REMARK 500 O HOH A 289 O HOH A 295 1.37 REMARK 500 O HOH C 270 O HOH C 272 1.40 REMARK 500 O HOH F 266 O HOH F 296 1.41 REMARK 500 O HOH B 296 O HOH B 308 1.44 REMARK 500 O HOH C 291 O HOH C 292 1.47 REMARK 500 O HOH D 281 O HOH D 292 1.48 REMARK 500 O HOH F 283 O HOH F 294 1.48 REMARK 500 O HOH D 215 O HOH D 230 1.48 REMARK 500 O HOH D 271 O HOH D 293 1.48 REMARK 500 O HOH D 229 O HOH D 262 1.48 REMARK 500 O LYS F 16 O HOH F 201 1.48 REMARK 500 O HOH E 205 O HOH E 224 1.50 REMARK 500 O HOH F 259 O HOH F 294 1.54 REMARK 500 O HOH A 264 O HOH A 270 1.54 REMARK 500 O LYS D 16 O HOH D 201 1.54 REMARK 500 OG1 THR F 44 O HOH F 202 1.55 REMARK 500 O HOH A 287 O HOH A 308 1.58 REMARK 500 O HOH C 283 O HOH C 309 1.58 REMARK 500 O HOH E 230 O HOH B 216 1.61 REMARK 500 O HOH F 283 O HOH F 285 1.61 REMARK 500 O HOH E 269 O HOH E 282 1.62 REMARK 500 O HOH E 203 O HOH E 204 1.64 REMARK 500 O HOH F 274 O HOH F 287 1.64 REMARK 500 O HOH A 288 O HOH A 329 1.64 REMARK 500 O HOH F 201 O HOH F 236 1.68 REMARK 500 O LYS B 60 O HOH B 201 1.69 REMARK 500 O HOH A 222 O HOH A 284 1.69 REMARK 500 O HOH F 262 O HOH F 270 1.69 REMARK 500 O HOH A 285 O HOH A 300 1.69 REMARK 500 N GLY F 41 O HOH F 203 1.70 REMARK 500 O HOH A 205 O HOH A 234 1.70 REMARK 500 O HOH C 287 O HOH C 301 1.71 REMARK 500 O HOH F 230 O HOH F 262 1.72 REMARK 500 O HOH D 234 O HOH D 272 1.72 REMARK 500 OE2 GLU C 82 O HOH C 201 1.73 REMARK 500 O LYS C 16 O HOH C 202 1.73 REMARK 500 O LYS A 16 O HOH A 201 1.74 REMARK 500 O HOH C 287 O HOH C 289 1.75 REMARK 500 O HOH B 278 O HOH B 306 1.76 REMARK 500 O HOH A 206 O HOH A 240 1.76 REMARK 500 N GLY E 41 O HOH E 201 1.79 REMARK 500 REMARK 500 THIS ENTRY HAS 95 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 O HOH F 299 O HOH D 288 7655 1.53 REMARK 500 O HOH A 291 O HOH F 209 7545 1.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 52 CD GLU A 52 OE2 -0.067 REMARK 500 GLU B 8 CD GLU B 8 OE1 -0.069 REMARK 500 GLU B 52 CD GLU B 52 OE2 -0.079 REMARK 500 GLU D 8 CD GLU D 8 OE1 -0.072 REMARK 500 GLU D 52 CD GLU D 52 OE2 -0.086 REMARK 500 GLU D 56 CD GLU D 56 OE1 -0.073 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 LYS A 43 -157.59 -97.28 REMARK 500 LYS C 43 -144.53 -107.54 REMARK 500 LYS E 43 -157.99 -102.99 REMARK 500 LYS F 43 -137.71 -91.32 REMARK 500 LYS F 43 -141.17 -87.43 REMARK 500 ALA B 9 155.93 -49.98 REMARK 500 LYS B 43 -131.68 -111.44 REMARK 500 LYS D 43 -146.68 -102.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 VAL C 6 10.19 REMARK 500 VAL C 6 10.04 REMARK 500 GLY C 17 -10.30 REMARK 500 VAL C 19 11.01 REMARK 500 VAL C 19 10.86 REMARK 500 VAL E 19 11.31 REMARK 500 VAL E 19 11.87 REMARK 500 ARG D 5 12.57 REMARK 500 ARG D 5 12.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 332 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A 333 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH C 326 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH E 297 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH E 298 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH E 299 DISTANCE = 7.43 ANGSTROMS REMARK 525 HOH B 333 DISTANCE = 6.30 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL C 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL C 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL E 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT F 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL D 102 DBREF 7DVC A -1 85 PDB 7DVC 7DVC -1 85 DBREF 7DVC C -1 85 PDB 7DVC 7DVC -1 85 DBREF 7DVC E -1 85 PDB 7DVC 7DVC -1 85 DBREF 7DVC F -1 85 PDB 7DVC 7DVC -1 85 DBREF 7DVC B -1 85 PDB 7DVC 7DVC -1 85 DBREF 7DVC D -1 85 PDB 7DVC 7DVC -1 85 SEQRES 1 A 87 GLY PRO PRO ILE LYS LEU ARG VAL MET GLU ALA TYR PRO SEQRES 2 A 87 GLU ASP VAL GLY LYS GLY ILE VAL ARG MET ASP LYS ALA SEQRES 3 A 87 SER ARG ASP LYS LEU GLY VAL SER ALA GLY ASP LEU VAL SEQRES 4 A 87 GLU ILE LYS GLY SER LYS THR PRO ILE LYS LEU ARG VAL SEQRES 5 A 87 MET GLU ALA TYR PRO GLU ASP VAL GLY LYS GLY ILE VAL SEQRES 6 A 87 ARG MET ASP LYS ALA SER ARG ASP LYS LEU GLY VAL SER SEQRES 7 A 87 ALA GLY ASP LEU VAL GLU ILE LYS GLY SEQRES 1 C 87 GLY PRO PRO ILE LYS LEU ARG VAL MET GLU ALA TYR PRO SEQRES 2 C 87 GLU ASP VAL GLY LYS GLY ILE VAL ARG MET ASP LYS ALA SEQRES 3 C 87 SER ARG ASP LYS LEU GLY VAL SER ALA GLY ASP LEU VAL SEQRES 4 C 87 GLU ILE LYS GLY SER LYS THR PRO ILE LYS LEU ARG VAL SEQRES 5 C 87 MET GLU ALA TYR PRO GLU ASP VAL GLY LYS GLY ILE VAL SEQRES 6 C 87 ARG MET ASP LYS ALA SER ARG ASP LYS LEU GLY VAL SER SEQRES 7 C 87 ALA GLY ASP LEU VAL GLU ILE LYS GLY SEQRES 1 E 87 GLY PRO PRO ILE LYS LEU ARG VAL MET GLU ALA TYR PRO SEQRES 2 E 87 GLU ASP VAL GLY LYS GLY ILE VAL ARG MET ASP LYS ALA SEQRES 3 E 87 SER ARG ASP LYS LEU GLY VAL SER ALA GLY ASP LEU VAL SEQRES 4 E 87 GLU ILE LYS GLY SER LYS THR PRO ILE LYS LEU ARG VAL SEQRES 5 E 87 MET GLU ALA TYR PRO GLU ASP VAL GLY LYS GLY ILE VAL SEQRES 6 E 87 ARG MET ASP LYS ALA SER ARG ASP LYS LEU GLY VAL SER SEQRES 7 E 87 ALA GLY ASP LEU VAL GLU ILE LYS GLY SEQRES 1 F 87 GLY PRO PRO ILE LYS LEU ARG VAL MET GLU ALA TYR PRO SEQRES 2 F 87 GLU ASP VAL GLY LYS GLY ILE VAL ARG MET ASP LYS ALA SEQRES 3 F 87 SER ARG ASP LYS LEU GLY VAL SER ALA GLY ASP LEU VAL SEQRES 4 F 87 GLU ILE LYS GLY SER LYS THR PRO ILE LYS LEU ARG VAL SEQRES 5 F 87 MET GLU ALA TYR PRO GLU ASP VAL GLY LYS GLY ILE VAL SEQRES 6 F 87 ARG MET ASP LYS ALA SER ARG ASP LYS LEU GLY VAL SER SEQRES 7 F 87 ALA GLY ASP LEU VAL GLU ILE LYS GLY SEQRES 1 B 87 GLY PRO PRO ILE LYS LEU ARG VAL MET GLU ALA TYR PRO SEQRES 2 B 87 GLU ASP VAL GLY LYS GLY ILE VAL ARG MET ASP LYS ALA SEQRES 3 B 87 SER ARG ASP LYS LEU GLY VAL SER ALA GLY ASP LEU VAL SEQRES 4 B 87 GLU ILE LYS GLY SER LYS THR PRO ILE LYS LEU ARG VAL SEQRES 5 B 87 MET GLU ALA TYR PRO GLU ASP VAL GLY LYS GLY ILE VAL SEQRES 6 B 87 ARG MET ASP LYS ALA SER ARG ASP LYS LEU GLY VAL SER SEQRES 7 B 87 ALA GLY ASP LEU VAL GLU ILE LYS GLY SEQRES 1 D 87 GLY PRO PRO ILE LYS LEU ARG VAL MET GLU ALA TYR PRO SEQRES 2 D 87 GLU ASP VAL GLY LYS GLY ILE VAL ARG MET ASP LYS ALA SEQRES 3 D 87 SER ARG ASP LYS LEU GLY VAL SER ALA GLY ASP LEU VAL SEQRES 4 D 87 GLU ILE LYS GLY SER LYS THR PRO ILE LYS LEU ARG VAL SEQRES 5 D 87 MET GLU ALA TYR PRO GLU ASP VAL GLY LYS GLY ILE VAL SEQRES 6 D 87 ARG MET ASP LYS ALA SER ARG ASP LYS LEU GLY VAL SER SEQRES 7 D 87 ALA GLY ASP LEU VAL GLU ILE LYS GLY HET CL A 101 1 HET CL A 102 1 HET CL A 103 1 HET ACT C 101 4 HET CL C 102 1 HET CL C 103 1 HET CL C 104 1 HET ACT E 101 4 HET CL E 102 1 HET ACT F 101 4 HET ACT B 101 4 HET CL B 102 1 HET ACT D 101 4 HET CL D 102 1 HETNAM CL CHLORIDE ION HETNAM ACT ACETATE ION FORMUL 7 CL 9(CL 1-) FORMUL 10 ACT 5(C2 H3 O2 1-) FORMUL 21 HOH *716(H2 O) HELIX 1 AA1 TYR A 10 VAL A 14 5 5 HELIX 2 AA2 ASP A 22 GLY A 30 1 9 HELIX 3 AA3 TYR A 54 VAL A 58 5 5 HELIX 4 AA4 ASP A 66 GLY A 74 1 9 HELIX 5 AA5 TYR C 10 VAL C 14 5 5 HELIX 6 AA6 ASP C 22 GLY C 30 1 9 HELIX 7 AA7 TYR C 54 VAL C 58 5 5 HELIX 8 AA8 ASP C 66 GLY C 74 1 9 HELIX 9 AA9 TYR E 10 VAL E 14 5 5 HELIX 10 AB1 ASP E 22 GLY E 30 1 9 HELIX 11 AB2 TYR E 54 VAL E 58 5 5 HELIX 12 AB3 ASP E 66 GLY E 74 1 9 HELIX 13 AB4 TYR F 10 VAL F 14 5 5 HELIX 14 AB5 ASP F 22 GLY F 30 1 9 HELIX 15 AB6 TYR F 54 VAL F 58 5 5 HELIX 16 AB7 ASP F 66 GLY F 74 1 9 HELIX 17 AB8 TYR B 10 VAL B 14 5 5 HELIX 18 AB9 ASP B 22 GLY B 30 1 9 HELIX 19 AC1 TYR B 54 VAL B 58 5 5 HELIX 20 AC2 ASP B 66 GLY B 74 1 9 HELIX 21 AC3 TYR D 10 VAL D 14 5 5 HELIX 22 AC4 ASP D 22 GLY D 30 1 9 HELIX 23 AC5 TYR D 54 VAL D 58 5 5 HELIX 24 AC6 ASP D 66 GLY D 74 1 9 SHEET 1 AA1 7 ILE A 2 GLU A 8 0 SHEET 2 AA1 7 ILE A 62 MET A 65 1 O VAL A 63 N MET A 7 SHEET 3 AA1 7 ILE A 18 MET A 21 -1 N ARG A 20 O ARG A 64 SHEET 4 AA1 7 ILE A 46 GLU A 52 1 O ARG A 49 N VAL A 19 SHEET 5 AA1 7 LEU A 36 LYS A 40 -1 N ILE A 39 O ILE A 46 SHEET 6 AA1 7 LEU A 80 LYS A 84 -1 O LYS A 84 N GLU A 38 SHEET 7 AA1 7 ILE A 2 GLU A 8 -1 N LEU A 4 O VAL A 81 SHEET 1 AA2 7 ILE C 2 GLU C 8 0 SHEET 2 AA2 7 ILE C 62 MET C 65 1 O VAL C 63 N MET C 7 SHEET 3 AA2 7 ILE C 18 MET C 21 -1 N ARG C 20 O ARG C 64 SHEET 4 AA2 7 ILE C 46 GLU C 52 1 O MET C 51 N VAL C 19 SHEET 5 AA2 7 LEU C 36 LYS C 40 -1 N ILE C 39 O ILE C 46 SHEET 6 AA2 7 LEU C 80 LYS C 84 -1 O LYS C 84 N GLU C 38 SHEET 7 AA2 7 ILE C 2 GLU C 8 -1 N ILE C 2 O ILE C 83 SHEET 1 AA3 7 ILE E 2 GLU E 8 0 SHEET 2 AA3 7 ILE E 62 MET E 65 1 O VAL E 63 N MET E 7 SHEET 3 AA3 7 ILE E 18 MET E 21 -1 N ARG E 20 O ARG E 64 SHEET 4 AA3 7 ILE E 46 GLU E 52 1 O MET E 51 N VAL E 19 SHEET 5 AA3 7 LEU E 36 LYS E 40 -1 N ILE E 39 O ILE E 46 SHEET 6 AA3 7 LEU E 80 LYS E 84 -1 O LYS E 84 N GLU E 38 SHEET 7 AA3 7 ILE E 2 GLU E 8 -1 N LEU E 4 O VAL E 81 SHEET 1 AA4 7 PRO F 1 GLU F 8 0 SHEET 2 AA4 7 ILE F 62 MET F 65 1 O VAL F 63 N ARG F 5 SHEET 3 AA4 7 ILE F 18 MET F 21 -1 N ARG F 20 O ARG F 64 SHEET 4 AA4 7 ILE F 46 GLU F 52 1 O MET F 51 N VAL F 19 SHEET 5 AA4 7 LEU F 36 LYS F 40 -1 N ILE F 39 O ILE F 46 SHEET 6 AA4 7 LEU F 80 LYS F 84 -1 O LYS F 84 N GLU F 38 SHEET 7 AA4 7 PRO F 1 GLU F 8 -1 N ILE F 2 O ILE F 83 SHEET 1 AA5 7 ILE B 2 GLU B 8 0 SHEET 2 AA5 7 ILE B 62 MET B 65 1 O MET B 65 N MET B 7 SHEET 3 AA5 7 ILE B 18 MET B 21 -1 N ARG B 20 O ARG B 64 SHEET 4 AA5 7 ILE B 46 GLU B 52 1 O MET B 51 N VAL B 19 SHEET 5 AA5 7 LEU B 36 LYS B 40 -1 N ILE B 39 O ILE B 46 SHEET 6 AA5 7 LEU B 80 LYS B 84 -1 O GLU B 82 N LYS B 40 SHEET 7 AA5 7 ILE B 2 GLU B 8 -1 N ILE B 2 O ILE B 83 SHEET 1 AA6 7 ILE D 2 GLU D 8 0 SHEET 2 AA6 7 ILE D 62 MET D 65 1 O VAL D 63 N ARG D 5 SHEET 3 AA6 7 ILE D 18 MET D 21 -1 N ARG D 20 O ARG D 64 SHEET 4 AA6 7 ILE D 46 GLU D 52 1 O MET D 51 N MET D 21 SHEET 5 AA6 7 LEU D 36 LYS D 40 -1 N ILE D 39 O ILE D 46 SHEET 6 AA6 7 LEU D 80 LYS D 84 -1 O GLU D 82 N LYS D 40 SHEET 7 AA6 7 ILE D 2 GLU D 8 -1 N ILE D 2 O ILE D 83 SITE 1 AC1 5 ASP A 22 LYS A 23 ARG A 26 HOH A 256 SITE 2 AC1 5 HOH A 288 SITE 1 AC2 4 LYS A 43 HOH A 311 ARG F 49 MET F 51 SITE 1 AC3 4 ARG A 49 MET A 51 HOH A 302 LYS C 43 SITE 1 AC4 7 GLU C 52 ALA C 53 PRO C 55 VAL C 58 SITE 2 AC4 7 HOH C 236 HOH C 269 ARG F 70 SITE 1 AC5 4 HOH A 273 GLU C 8 ARG C 70 HOH C 296 SITE 1 AC6 6 LYS A 23 HOH A 230 ILE B 46 LYS B 47 SITE 2 AC6 6 HOH B 226 ARG C 5 SITE 1 AC7 3 LYS B 72 ASP C 79 LEU C 80 SITE 1 AC8 7 ARG D 70 CL D 102 GLU E 52 ALA E 53 SITE 2 AC8 7 PRO E 55 VAL E 58 CL E 102 SITE 1 AC9 5 ASP E 22 LYS E 23 ARG E 26 ACT E 101 SITE 2 AC9 5 HOH E 264 SITE 1 AD1 5 ARG A 70 GLU F 52 ALA F 53 PRO F 55 SITE 2 AD1 5 HOH F 226 SITE 1 AD2 7 GLU B 8 ALA B 9 PRO B 11 VAL B 14 SITE 2 AD2 7 HOH B 242 HOH B 264 ARG E 70 SITE 1 AD3 4 ARG B 5 MET B 7 HOH B 309 LYS E 43 SITE 1 AD4 6 ARG B 26 GLU D 52 ALA D 53 PRO D 55 SITE 2 AD4 6 VAL D 58 HOH D 228 SITE 1 AD5 4 GLU D 8 ARG D 70 ACT E 101 GLU F 12 CRYST1 98.151 98.151 177.324 90.00 90.00 90.00 P 43 21 2 48 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 0.010188 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010188 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005639 0.00000