HEADER IMMUNE SYSTEM 01-JUN-20 6X8Q TITLE CRYSTAL STRUCTURE OF 3D11 FAB IN COMPLEX WITH PLASMODIUM BERGHEI TITLE 2 CIRCUMSPOROZOITE PROTEIN PAPP PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3D11 FAB HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 3D11 FAB LIGHT CHAIN; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PAPP PEPTIDE; COMPND 11 CHAIN: P; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_COMMON: MOUSE; SOURCE 11 ORGANISM_TAXID: 10090; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: PLASMODIUM BERGHEI ANKA; SOURCE 18 ORGANISM_TAXID: 5823 KEYWDS MALARIA, ANTIBODY, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR E.THAI,J.P.JULIEN REVDAT 3 03-APR-24 6X8Q 1 REMARK REVDAT 2 30-DEC-20 6X8Q 1 JRNL REVDAT 1 02-DEC-20 6X8Q 0 JRNL AUTH I.KUCHARSKA,E.THAI,A.SRIVASTAVA,J.L.RUBINSTEIN,R.POMES, JRNL AUTH 2 J.P.JULIEN JRNL TITL STRUCTURAL ORDERING OF THE PLASMODIUM BERGHEI JRNL TITL 2 CIRCUMSPOROZOITE PROTEIN REPEATS BY INHIBITORY ANTIBODY JRNL TITL 3 3D11. JRNL REF ELIFE V. 9 2020 JRNL REFN ESSN 2050-084X JRNL PMID 33253113 JRNL DOI 10.7554/ELIFE.59018 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 64275 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.110 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 19.6200 - 3.8500 1.00 4790 159 0.1424 0.1513 REMARK 3 2 3.8500 - 3.0600 1.00 4555 149 0.1415 0.1648 REMARK 3 3 3.0600 - 2.6700 1.00 4493 142 0.1591 0.1930 REMARK 3 4 2.6700 - 2.4300 1.00 4473 142 0.1642 0.2025 REMARK 3 5 2.4300 - 2.2500 1.00 4460 144 0.1624 0.2279 REMARK 3 6 2.2500 - 2.1200 1.00 4382 139 0.1640 0.1808 REMARK 3 7 2.1200 - 2.0200 1.00 4432 142 0.1581 0.2081 REMARK 3 8 2.0200 - 1.9300 1.00 4404 144 0.1674 0.1978 REMARK 3 9 1.9300 - 1.8500 1.00 4381 137 0.1805 0.2348 REMARK 3 10 1.8500 - 1.7900 1.00 4409 141 0.2174 0.2723 REMARK 3 11 1.7900 - 1.7300 1.00 4411 142 0.2079 0.2497 REMARK 3 12 1.7300 - 1.6800 1.00 4353 139 0.2167 0.2841 REMARK 3 13 1.6800 - 1.6400 1.00 4398 142 0.2330 0.2793 REMARK 3 14 1.6400 - 1.6000 1.00 4335 137 0.2508 0.2626 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) : 0.166 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.022 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.00 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 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 : 0.016 3531 REMARK 3 ANGLE : 1.431 4830 REMARK 3 CHIRALITY : 0.111 558 REMARK 3 PLANARITY : 0.010 616 REMARK 3 DIHEDRAL : 11.461 2167 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 3 THROUGH 113) REMARK 3 ORIGIN FOR THE GROUP (A): 41.0344 -25.5848 -67.8668 REMARK 3 T TENSOR REMARK 3 T11: 0.1384 T22: 0.2365 REMARK 3 T33: 0.1934 T12: 0.0090 REMARK 3 T13: -0.0265 T23: -0.0407 REMARK 3 L TENSOR REMARK 3 L11: 1.8008 L22: 2.9398 REMARK 3 L33: 3.8351 L12: 0.7079 REMARK 3 L13: -0.7868 L23: -1.0862 REMARK 3 S TENSOR REMARK 3 S11: 0.0137 S12: 0.0318 S13: -0.0347 REMARK 3 S21: 0.0719 S22: -0.0541 S23: 0.1089 REMARK 3 S31: 0.0645 S32: -0.0609 S33: 0.0266 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 114 THROUGH 211 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.9384 -18.8765 -39.7464 REMARK 3 T TENSOR REMARK 3 T11: 0.1943 T22: 0.2438 REMARK 3 T33: 0.2773 T12: -0.0243 REMARK 3 T13: -0.0089 T23: 0.0142 REMARK 3 L TENSOR REMARK 3 L11: 1.2452 L22: 5.9629 REMARK 3 L33: 2.2039 L12: -1.3451 REMARK 3 L13: -0.7277 L23: 2.3275 REMARK 3 S TENSOR REMARK 3 S11: -0.0599 S12: 0.0408 S13: -0.1028 REMARK 3 S21: 0.0318 S22: -0.0313 S23: 0.3288 REMARK 3 S31: 0.0842 S32: -0.1780 S33: 0.1333 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 1 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): 58.3806 -12.5077 -62.7341 REMARK 3 T TENSOR REMARK 3 T11: 0.1737 T22: 0.2689 REMARK 3 T33: 0.1925 T12: -0.0258 REMARK 3 T13: 0.0010 T23: 0.0040 REMARK 3 L TENSOR REMARK 3 L11: 1.1429 L22: 2.7766 REMARK 3 L33: 3.5842 L12: 0.2188 REMARK 3 L13: 0.2134 L23: 2.2778 REMARK 3 S TENSOR REMARK 3 S11: 0.0377 S12: 0.0419 S13: 0.0570 REMARK 3 S21: 0.0172 S22: -0.0437 S23: -0.0291 REMARK 3 S31: -0.0091 S32: 0.0676 S33: 0.0103 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 108 THROUGH 214 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.6425 -20.2874 -27.9390 REMARK 3 T TENSOR REMARK 3 T11: 0.2166 T22: 0.1938 REMARK 3 T33: 0.2239 T12: 0.0016 REMARK 3 T13: 0.0163 T23: 0.0026 REMARK 3 L TENSOR REMARK 3 L11: 2.6138 L22: 2.7302 REMARK 3 L33: 3.0710 L12: 1.4098 REMARK 3 L13: -1.4363 L23: -0.8570 REMARK 3 S TENSOR REMARK 3 S11: -0.0122 S12: -0.1444 S13: -0.1355 REMARK 3 S21: 0.2369 S22: -0.0043 S23: 0.1390 REMARK 3 S31: 0.2068 S32: -0.0197 S33: 0.0488 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 13 ) REMARK 3 ORIGIN FOR THE GROUP (A): 48.3008 -12.7583 -78.6073 REMARK 3 T TENSOR REMARK 3 T11: 0.3178 T22: 0.4326 REMARK 3 T33: 0.2443 T12: 0.0226 REMARK 3 T13: -0.0814 T23: 0.0332 REMARK 3 L TENSOR REMARK 3 L11: 4.0676 L22: 1.0507 REMARK 3 L33: 2.0770 L12: 0.4539 REMARK 3 L13: -0.5802 L23: 0.1372 REMARK 3 S TENSOR REMARK 3 S11: -0.1615 S12: 1.0319 S13: 0.3015 REMARK 3 S21: -0.7114 S22: -0.1778 S23: 0.4751 REMARK 3 S31: -0.4681 S32: -0.2705 S33: 0.3479 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 6X8Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000249776. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-APR-19 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 : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033170 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64371 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 18.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 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: INTERNAL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 3350, 0.15 M MALIC ACID REMARK 280 PH 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 155.69467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 77.84733 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 77.84733 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 155.69467 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, P REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 O1 EDO L 302 LIES ON A SPECIAL POSITION. REMARK 375 HOH L 607 LIES ON A SPECIAL POSITION. 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 GLN H 1 REMARK 465 ALA H 2 REMARK 465 ALA P 14 REMARK 465 ASN P 15 REMARK 465 ASP P 16 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN H 61 CG CD OE1 NE2 REMARK 470 GLU L 143 CG CD OE1 OE2 REMARK 470 GLU L 213 CG CD OE1 OE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 VAL L 163 CA CB CG1 CG2 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 L 527 O HOH L 576 2.03 REMARK 500 O ALA H 101 O HOH H 401 2.18 REMARK 500 O HOH H 452 O HOH H 554 2.19 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 SER H 188 CB SER H 188 OG 0.131 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 LEU L 33 CA - CB - CG ANGL. DEV. = -15.0 DEGREES REMARK 500 ARG L 61 NE - CZ - NH2 ANGL. DEV. = -4.1 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 ALA H 95 -130.26 54.33 REMARK 500 ASP H 144 53.30 72.20 REMARK 500 VAL L 51 -51.08 77.05 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 L 610 DISTANCE = 6.26 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO H 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO H 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO H 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO H 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO L 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO L 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO P 101 DBREF 6X8Q H 1 216 PDB 6X8Q 6X8Q 1 216 DBREF 6X8Q L 1 214 PDB 6X8Q 6X8Q 1 214 DBREF 6X8Q P 1 16 PDB 6X8Q 6X8Q 1 16 SEQRES 1 H 215 GLN ALA TYR LEU GLN GLN SER GLY ALA GLU LEU VAL ARG SEQRES 2 H 215 SER GLY ALA SER VAL LYS MET SER CYS LYS ALA SER GLY SEQRES 3 H 215 TYR THR PHE THR SER TYR ASN MET HIS TRP VAL LYS GLN SEQRES 4 H 215 THR PRO GLY GLN GLY LEU GLU TRP ILE GLY TYR ILE TYR SEQRES 5 H 215 PRO GLY ASN GLY VAL THR ASN PHE ASN GLN LYS PHE LYS SEQRES 6 H 215 GLY LYS ALA THR LEU THR ALA ASP THR SER SER SER THR SEQRES 7 H 215 ALA TYR MET GLN ILE SER SER LEU THR SER GLU ASP SER SEQRES 8 H 215 ALA VAL TYR PHE CYS ALA SER ALA ALA TYR TRP GLY GLN SEQRES 9 H 215 GLY THR LEU VAL THR VAL SER SER ALA SER THR LYS GLY SEQRES 10 H 215 PRO SER VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SEQRES 11 H 215 SER GLY GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP SEQRES 12 H 215 TYR PHE PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY SEQRES 13 H 215 ALA LEU THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU SEQRES 14 H 215 GLN SER SER GLY LEU TYR SER LEU SER SER VAL VAL THR SEQRES 15 H 215 VAL PRO SER SER SER LEU GLY THR GLN THR TYR ILE CYS SEQRES 16 H 215 ASN VAL ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS SEQRES 17 H 215 LYS VAL GLU PRO LYS SER CYS SEQRES 1 L 219 ASP VAL VAL MET THR GLN THR PRO LEU THR LEU SER VAL SEQRES 2 L 219 THR ILE GLY GLN PRO ALA SER ILE SER CYS LYS SER SER SEQRES 3 L 219 GLN SER LEU LEU TYR SER ASP GLY LYS THR TYR LEU ASN SEQRES 4 L 219 TRP LEU LEU GLN ARG PRO GLY GLN SER PRO LYS ARG LEU SEQRES 5 L 219 ILE SER LEU VAL SER GLU LEU ASP SER GLY VAL PRO ASP SEQRES 6 L 219 ARG PHE THR GLY SER GLY SER GLY THR ASP PHE THR LEU SEQRES 7 L 219 LYS ILE SER ARG VAL GLU ALA GLU ASP LEU GLY VAL TYR SEQRES 8 L 219 TYR CYS TRP GLN GLY THR HIS PHE PRO ARG THR PHE GLY SEQRES 9 L 219 GLY GLY THR LYS LEU GLU ILE LYS ARG THR VAL ALA ALA SEQRES 10 L 219 PRO SER VAL PHE ILE PHE PRO PRO SER ASP GLU GLN LEU SEQRES 11 L 219 LYS SER GLY THR ALA SER VAL VAL CYS LEU LEU ASN ASN SEQRES 12 L 219 PHE TYR PRO ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP SEQRES 13 L 219 ASN ALA LEU GLN SER GLY ASN SER GLN GLU SER VAL THR SEQRES 14 L 219 GLU GLN ASP SER LYS ASP SER THR TYR SER LEU SER SER SEQRES 15 L 219 THR LEU THR LEU SER LYS ALA ASP TYR GLU LYS HIS LYS SEQRES 16 L 219 VAL TYR ALA CYS GLU VAL THR HIS GLN GLY LEU SER SER SEQRES 17 L 219 PRO VAL THR LYS SER PHE ASN ARG GLY GLU CYS SEQRES 1 P 16 PRO ALA PRO PRO ASN ALA ASN ASP PRO ALA PRO PRO ASN SEQRES 2 P 16 ALA ASN ASP HET EDO H 301 4 HET EDO H 302 4 HET EDO H 303 4 HET EDO H 304 4 HET EDO L 301 4 HET EDO L 302 4 HET EDO P 101 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 EDO 7(C2 H6 O2) FORMUL 11 HOH *384(H2 O) HELIX 1 AA1 THR H 28 TYR H 32 5 5 HELIX 2 AA2 GLN H 61 LYS H 64 5 4 HELIX 3 AA3 THR H 83 SER H 87 5 5 HELIX 4 AA4 SER H 127 LYS H 129 5 3 HELIX 5 AA5 SER H 156 ALA H 158 5 3 HELIX 6 AA6 SER H 187 LEU H 189 5 3 HELIX 7 AA7 LYS H 201 ASN H 204 5 4 HELIX 8 AA8 GLU L 79 LEU L 83 5 5 HELIX 9 AA9 SER L 121 SER L 127 1 7 HELIX 10 AB1 LYS L 183 GLU L 187 1 5 SHEET 1 AA1 4 LEU H 4 GLN H 6 0 SHEET 2 AA1 4 VAL H 18 ALA H 24 -1 O LYS H 23 N GLN H 5 SHEET 3 AA1 4 THR H 77 ILE H 82 -1 O ALA H 78 N CYS H 22 SHEET 4 AA1 4 ALA H 67 ASP H 72 -1 N ASP H 72 O THR H 77 SHEET 1 AA2 6 GLU H 10 VAL H 12 0 SHEET 2 AA2 6 THR H 107 VAL H 111 1 O THR H 110 N GLU H 10 SHEET 3 AA2 6 ALA H 88 SER H 94 -1 N ALA H 88 O VAL H 109 SHEET 4 AA2 6 MET H 34 GLN H 39 -1 N VAL H 37 O PHE H 91 SHEET 5 AA2 6 LEU H 45 ILE H 51 -1 O ILE H 51 N MET H 34 SHEET 6 AA2 6 THR H 57 PHE H 59 -1 O ASN H 58 N TYR H 50 SHEET 1 AA3 4 GLU H 10 VAL H 12 0 SHEET 2 AA3 4 THR H 107 VAL H 111 1 O THR H 110 N GLU H 10 SHEET 3 AA3 4 ALA H 88 SER H 94 -1 N ALA H 88 O VAL H 109 SHEET 4 AA3 4 TYR H 102 TRP H 103 -1 O TYR H 102 N SER H 94 SHEET 1 AA4 4 SER H 120 LEU H 124 0 SHEET 2 AA4 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AA4 4 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 4 AA4 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 AA5 4 THR H 131 SER H 132 0 SHEET 2 AA5 4 THR H 135 TYR H 145 -1 O THR H 135 N SER H 132 SHEET 3 AA5 4 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 4 AA5 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 AA6 3 THR H 151 TRP H 154 0 SHEET 2 AA6 3 ILE H 195 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 AA6 3 THR H 205 LYS H 210 -1 O VAL H 207 N VAL H 198 SHEET 1 AA7 4 MET L 4 THR L 7 0 SHEET 2 AA7 4 ALA L 19 SER L 25 -1 O LYS L 24 N THR L 5 SHEET 3 AA7 4 ASP L 70 ILE L 75 -1 O ILE L 75 N ALA L 19 SHEET 4 AA7 4 PHE L 62 SER L 67 -1 N THR L 63 O LYS L 74 SHEET 1 AA8 6 THR L 10 THR L 14 0 SHEET 2 AA8 6 THR L 102 LYS L 107 1 O LYS L 107 N VAL L 13 SHEET 3 AA8 6 GLY L 84 GLN L 90 -1 N GLY L 84 O LEU L 104 SHEET 4 AA8 6 LEU L 33 GLN L 38 -1 N LEU L 36 O TYR L 87 SHEET 5 AA8 6 PRO L 44 SER L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AA8 6 GLU L 53 LEU L 54 -1 O GLU L 53 N SER L 49 SHEET 1 AA9 4 THR L 10 THR L 14 0 SHEET 2 AA9 4 THR L 102 LYS L 107 1 O LYS L 107 N VAL L 13 SHEET 3 AA9 4 GLY L 84 GLN L 90 -1 N GLY L 84 O LEU L 104 SHEET 4 AA9 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 AB1 4 SER L 114 PHE L 118 0 SHEET 2 AB1 4 THR L 129 PHE L 139 -1 O LEU L 135 N PHE L 116 SHEET 3 AB1 4 TYR L 173 SER L 182 -1 O LEU L 175 N LEU L 136 SHEET 4 AB1 4 SER L 159 VAL L 163 -1 N SER L 162 O SER L 176 SHEET 1 AB2 4 ALA L 153 LEU L 154 0 SHEET 2 AB2 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 AB2 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 AB2 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SSBOND 1 CYS H 22 CYS H 92 1555 1555 2.13 SSBOND 2 CYS H 140 CYS H 196 1555 1555 2.07 SSBOND 3 CYS H 216 CYS L 214 1555 1555 2.04 SSBOND 4 CYS L 23 CYS L 88 1555 1555 2.23 SSBOND 5 CYS L 134 CYS L 194 1555 1555 2.11 CISPEP 1 PHE H 146 PRO H 147 0 -4.16 CISPEP 2 GLU H 148 PRO H 149 0 -7.08 CISPEP 3 THR L 7 PRO L 8 0 -7.60 CISPEP 4 PHE L 94 PRO L 95 0 -0.91 CISPEP 5 TYR L 140 PRO L 141 0 6.45 SITE 1 AC1 8 ALA H 24 SER H 25 GLY H 26 TYR H 27 SITE 2 AC1 8 THR H 28 PHE H 29 SER H 76 HOH H 508 SITE 1 AC2 9 LEU H 141 VAL H 169 SER H 177 LEU H 178 SITE 2 AC2 9 SER H 179 HOH H 404 HOH H 435 HOH H 461 SITE 3 AC2 9 THR L 178 SITE 1 AC3 7 ASN H 155 GLN H 192 THR H 193 HOH H 405 SITE 2 AC3 7 ARG L 142 VAL L 163 HOH L 453 SITE 1 AC4 7 SER H 7 GLU H 10 LYS H 19 MET H 20 SITE 2 AC4 7 SER H 21 HOH H 402 HOH H 527 SITE 1 AC5 4 LEU L 9 GLY L 100 GLY L 101 HOH L 403 SITE 1 AC6 5 THR L 14 LYS L 107 ARG L 108 HOH L 478 SITE 2 AC6 5 HOH L 565 SITE 1 AC7 4 TYR L 32 ALA P 6 PRO P 9 ALA P 10 CRYST1 59.349 59.349 233.542 90.00 90.00 120.00 P 32 2 1 6 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 0.016849 0.009728 0.000000 0.00000 SCALE2 0.000000 0.019456 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004282 0.00000