HEADER IMMUNE SYSTEM 20-JUN-19 6PEF TITLE VACCINE-ELICITED NHP FP-TARGETING ANTIBODY DF2F-A.01 IN COMPLEX WITH TITLE 2 HIV FUSION PEPTIDE (RESIDUE 512-519) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIBODY DF2F-A.01 HEAVY CHAIN; COMPND 3 CHAIN: A, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ANTIBODY DF2F-A.01 LIGHT CHAIN; COMPND 7 CHAIN: B, E; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HIV FUSION PEPTIDE RESIDUE 512-519; COMPND 11 CHAIN: C, F; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 3 ORGANISM_TAXID: 9544; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 8 ORGANISM_TAXID: 9544; SOURCE 9 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 14 ORGANISM_TAXID: 11676 KEYWDS HIV, NEUTRALIZING, ANTIBODY, NHP, FP, FUSION PEPTIDE, VACCINE, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR K.XU,K.LIU,Y.WANG,P.D.KWONG REVDAT 1 24-JUN-20 6PEF 0 JRNL AUTH K.XU,K.LIU,Y.WANG,P.D.KWONG JRNL TITL MODULAR RECOGNITION OF ANTIGENS PROVIDES A MECHANISM THAT JRNL TITL 2 IMPROVES VACCINE-ELICITED ANTIBODY-CLASS FREQUENCIES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 75461 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.710 REMARK 3 FREE R VALUE TEST SET COUNT : 3552 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 43.1809 - 5.8538 0.98 3034 158 0.1761 0.1828 REMARK 3 2 5.8538 - 4.6481 0.99 2996 157 0.1465 0.1602 REMARK 3 3 4.6481 - 4.0611 0.99 2914 165 0.1366 0.1662 REMARK 3 4 4.0611 - 3.6900 0.99 2969 143 0.1595 0.1495 REMARK 3 5 3.6900 - 3.4256 0.99 2963 122 0.1719 0.2035 REMARK 3 6 3.4256 - 3.2237 0.99 2935 140 0.1831 0.2120 REMARK 3 7 3.2237 - 3.0623 0.99 2884 150 0.1861 0.2491 REMARK 3 8 3.0623 - 2.9290 0.99 2926 131 0.1889 0.2494 REMARK 3 9 2.9290 - 2.8163 0.98 2907 147 0.1913 0.2084 REMARK 3 10 2.8163 - 2.7191 0.98 2856 152 0.1898 0.2412 REMARK 3 11 2.7191 - 2.6341 0.98 2881 153 0.2044 0.2533 REMARK 3 12 2.6341 - 2.5588 0.98 2912 135 0.2028 0.2653 REMARK 3 13 2.5588 - 2.4915 0.98 2819 162 0.2072 0.3047 REMARK 3 14 2.4915 - 2.4307 0.98 2890 143 0.2045 0.2496 REMARK 3 15 2.4307 - 2.3755 0.98 2862 146 0.2159 0.2226 REMARK 3 16 2.3755 - 2.3249 0.98 2897 129 0.2144 0.2768 REMARK 3 17 2.3249 - 2.2784 0.97 2804 149 0.2103 0.2329 REMARK 3 18 2.2784 - 2.2354 0.97 2892 124 0.2183 0.2453 REMARK 3 19 2.2354 - 2.1955 0.97 2799 158 0.2151 0.2772 REMARK 3 20 2.1955 - 2.1583 0.97 2912 133 0.2154 0.2699 REMARK 3 21 2.1583 - 2.1235 0.97 2824 140 0.2243 0.3302 REMARK 3 22 2.1235 - 2.0908 0.97 2800 127 0.2381 0.2969 REMARK 3 23 2.0908 - 2.0600 0.97 2873 141 0.2377 0.2764 REMARK 3 24 2.0600 - 2.0310 0.96 2787 132 0.2417 0.2592 REMARK 3 25 2.0310 - 2.0036 0.87 2573 115 0.2513 0.3178 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.19 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 : 3 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN D REMARK 3 ATOM PAIRS NUMBER : 1320 REMARK 3 RMSD : NULL REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN B AND RESID 3 THROUGH 212) REMARK 3 SELECTION : CHAIN E REMARK 3 ATOM PAIRS NUMBER : 1260 REMARK 3 RMSD : NULL REMARK 3 NCS GROUP : 3 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN C REMARK 3 SELECTION : CHAIN F REMARK 3 ATOM PAIRS NUMBER : 42 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6PEF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1000242407. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-17 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 : 22-ID 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75515 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.66500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NACL, 0.1 M BIS-TRIS PH 6.5, 25% REMARK 280 PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 26.25200 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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: 2 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: 4660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, 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 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 A 1 REMARK 465 LYS A 221 REMARK 465 THR A 222 REMARK 465 CYS A 223 REMARK 465 GLY A 224 REMARK 465 GLY A 225 REMARK 465 GLY A 226 REMARK 465 GLN B 1 REMARK 465 ALA B 213 REMARK 465 GLU B 214 REMARK 465 CYS B 215 REMARK 465 SER B 216 REMARK 465 GLN D 1 REMARK 465 LYS D 221 REMARK 465 THR D 222 REMARK 465 CYS D 223 REMARK 465 GLY D 224 REMARK 465 GLY D 225 REMARK 465 GLY D 226 REMARK 465 GLN E 1 REMARK 465 SER E 2 REMARK 465 ALA E 213 REMARK 465 GLU E 214 REMARK 465 CYS E 215 REMARK 465 SER E 216 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 D 457 O HOH E 438 1.86 REMARK 500 O HOH A 368 O HOH A 448 1.87 REMARK 500 NE2 GLN E 130 O HOH E 301 1.89 REMARK 500 OG1 THR E 43 O HOH E 302 1.89 REMARK 500 OG1 THR A 75 O HOH A 301 1.93 REMARK 500 O HOH A 327 O HOH A 447 2.00 REMARK 500 O HOH A 348 O HOH A 429 2.01 REMARK 500 O HOH A 344 O HOH A 440 2.02 REMARK 500 OE2 GLU E 207 O HOH E 303 2.04 REMARK 500 O HOH A 414 O HOH A 438 2.05 REMARK 500 OG1 THR B 43 O HOH B 301 2.06 REMARK 500 O HOH B 372 O HOH B 460 2.08 REMARK 500 O HOH B 326 O HOH B 431 2.09 REMARK 500 O HOH A 377 O HOH A 439 2.09 REMARK 500 O HOH D 373 O HOH D 462 2.09 REMARK 500 OE2 GLU A 106 O HOH A 302 2.09 REMARK 500 O HOH B 471 O HOH B 473 2.09 REMARK 500 O HOH B 305 O HOH B 429 2.09 REMARK 500 O HOH E 419 O HOH E 441 2.09 REMARK 500 O HOH E 387 O HOH E 449 2.11 REMARK 500 O HOH A 306 O HOH A 350 2.12 REMARK 500 NE ARG A 103 O HOH A 303 2.13 REMARK 500 OE1 GLN B 198 O HOH B 302 2.13 REMARK 500 O HOH A 434 O HOH B 359 2.13 REMARK 500 O HOH E 461 O HOH E 468 2.14 REMARK 500 O HOH D 315 O HOH D 436 2.14 REMARK 500 N GLY E 58 O HOH E 304 2.14 REMARK 500 O HOH B 415 O HOH B 459 2.14 REMARK 500 O HOH A 377 O HOH A 409 2.15 REMARK 500 O HOH B 409 O HOH B 426 2.15 REMARK 500 O HOH E 332 O HOH E 447 2.18 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 A 442 O HOH B 427 2445 1.90 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 LYS A 77 CD - CE - NZ ANGL. DEV. = 14.2 DEGREES REMARK 500 LEU A 145 CA - CB - CG ANGL. DEV. = 17.2 DEGREES REMARK 500 CYS A 147 CA - CB - SG ANGL. DEV. = 9.8 DEGREES REMARK 500 CYS D 147 CA - CB - SG ANGL. DEV. = 6.9 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 SER A 15 -8.75 78.23 REMARK 500 ASN B 28 -78.44 -106.55 REMARK 500 SER B 52 -28.31 73.19 REMARK 500 ASN B 53 12.32 -147.08 REMARK 500 ASN B 174 -0.98 75.15 REMARK 500 SER D 15 -8.42 77.19 REMARK 500 ASN E 28 -78.10 -105.97 REMARK 500 SER E 52 -28.43 73.68 REMARK 500 ASN E 53 12.38 -146.04 REMARK 500 ASN E 174 -0.67 75.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG D 217 0.09 SIDE CHAIN 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 B 473 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH D 471 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH D 472 DISTANCE = 6.48 ANGSTROMS DBREF 6PEF A 1 226 PDB 6PEF 6PEF 1 226 DBREF 6PEF B 1 216 PDB 6PEF 6PEF 1 216 DBREF 6PEF C 512 519 PDB 6PEF 6PEF 512 519 DBREF 6PEF D 1 226 PDB 6PEF 6PEF 1 226 DBREF 6PEF E 1 216 PDB 6PEF 6PEF 1 216 DBREF 6PEF F 512 519 PDB 6PEF 6PEF 512 519 SEQRES 1 A 226 GLN VAL GLN LEU GLN GLU SER GLY PRO ALA VAL MET LYS SEQRES 2 A 226 PRO SER GLU THR LEU SER LEU THR CYS ALA VAL SER GLY SEQRES 3 A 226 GLY SER ILE SER GLY ASP TYR GLY TRP SER TRP ILE ARG SEQRES 4 A 226 GLN ALA PRO GLY LYS GLY LEU GLU TRP ILE ALA ILE ILE SEQRES 5 A 226 PHE GLY SER SER GLY SER THR TYR TYR SER PRO SER LEU SEQRES 6 A 226 LYS SER ARG VAL THR ILE SER LYS ASP THR SER LYS ASN SEQRES 7 A 226 GLN PHE SER LEU LYS LEU ASN SER VAL THR ALA ALA ASP SEQRES 8 A 226 THR ALA VAL TYR PHE CYS ALA GLY SER PRO VAL ARG GLN SEQRES 9 A 226 ARG GLU GLN ASP TYR TRP GLY GLN GLY VAL LEU VAL THR SEQRES 10 A 226 VAL SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO SEQRES 11 A 226 LEU ALA PRO SER SER ARG SER THR SER GLU SER THR ALA SEQRES 12 A 226 ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO SEQRES 13 A 226 VAL THR VAL SER TRP ASN SER GLY SER LEU THR SER GLY SEQRES 14 A 226 VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU SEQRES 15 A 226 TYR SER LEU SER SER VAL VAL THR VAL PRO SER SER SER SEQRES 16 A 226 LEU GLY THR GLN THR TYR VAL CYS ASN VAL ASN HIS LYS SEQRES 17 A 226 PRO SER ASN THR LYS VAL ASP LYS ARG VAL GLU ILE LYS SEQRES 18 A 226 THR CYS GLY GLY GLY SEQRES 1 B 216 GLN SER VAL LEU THR GLN PRO PRO SER VAL SER ALA ALA SEQRES 2 B 216 PRO GLY GLN LYS VAL THR ILE SER CYS SER GLY SER SER SEQRES 3 B 216 SER ASN ILE GLY ILE ASN TYR VAL ALA TRP TYR GLN GLN SEQRES 4 B 216 VAL PRO GLY THR ALA PRO LYS LEU LEU ILE TYR ASP SER SEQRES 5 B 216 ASN LYS ARG PRO SER GLY VAL SER ASP ARG PHE SER GLY SEQRES 6 B 216 SER LYS SER GLY ILE SER ALA SER LEU ALA ILE THR GLY SEQRES 7 B 216 LEU GLN THR GLY ASP GLU ALA ASP TYR TYR CYS GLY VAL SEQRES 8 B 216 TRP ASP THR SER LEU THR ALA TYR ILE PHE GLY ALA GLY SEQRES 9 B 216 THR ARG LEU THR VAL LEU GLY GLN PRO LYS ALA ALA PRO SEQRES 10 B 216 SER VAL THR LEU PHE PRO PRO SER SER GLU GLU LEU GLN SEQRES 11 B 216 ALA ASN LYS ALA THR LEU VAL CYS LEU ILE SER ASP PHE SEQRES 12 B 216 TYR PRO GLY ALA VAL GLU VAL ALA TRP LYS ALA ASP GLY SEQRES 13 B 216 SER ALA VAL ASN ALA GLY VAL GLU THR THR LYS PRO SER SEQRES 14 B 216 LYS GLN SER ASN ASN LYS TYR ALA ALA SER SER TYR LEU SEQRES 15 B 216 SER LEU THR SER ASP GLN TRP LYS SER HIS LYS SER TYR SEQRES 16 B 216 SER CYS GLN VAL THR HIS GLU GLY SER THR VAL GLU LYS SEQRES 17 B 216 THR VAL ALA PRO ALA GLU CYS SER SEQRES 1 C 8 ALA VAL GLY ILE GLY ALA VAL PHE SEQRES 1 D 226 GLN VAL GLN LEU GLN GLU SER GLY PRO ALA VAL MET LYS SEQRES 2 D 226 PRO SER GLU THR LEU SER LEU THR CYS ALA VAL SER GLY SEQRES 3 D 226 GLY SER ILE SER GLY ASP TYR GLY TRP SER TRP ILE ARG SEQRES 4 D 226 GLN ALA PRO GLY LYS GLY LEU GLU TRP ILE ALA ILE ILE SEQRES 5 D 226 PHE GLY SER SER GLY SER THR TYR TYR SER PRO SER LEU SEQRES 6 D 226 LYS SER ARG VAL THR ILE SER LYS ASP THR SER LYS ASN SEQRES 7 D 226 GLN PHE SER LEU LYS LEU ASN SER VAL THR ALA ALA ASP SEQRES 8 D 226 THR ALA VAL TYR PHE CYS ALA GLY SER PRO VAL ARG GLN SEQRES 9 D 226 ARG GLU GLN ASP TYR TRP GLY GLN GLY VAL LEU VAL THR SEQRES 10 D 226 VAL SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO SEQRES 11 D 226 LEU ALA PRO SER SER ARG SER THR SER GLU SER THR ALA SEQRES 12 D 226 ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO SEQRES 13 D 226 VAL THR VAL SER TRP ASN SER GLY SER LEU THR SER GLY SEQRES 14 D 226 VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU SEQRES 15 D 226 TYR SER LEU SER SER VAL VAL THR VAL PRO SER SER SER SEQRES 16 D 226 LEU GLY THR GLN THR TYR VAL CYS ASN VAL ASN HIS LYS SEQRES 17 D 226 PRO SER ASN THR LYS VAL ASP LYS ARG VAL GLU ILE LYS SEQRES 18 D 226 THR CYS GLY GLY GLY SEQRES 1 E 216 GLN SER VAL LEU THR GLN PRO PRO SER VAL SER ALA ALA SEQRES 2 E 216 PRO GLY GLN LYS VAL THR ILE SER CYS SER GLY SER SER SEQRES 3 E 216 SER ASN ILE GLY ILE ASN TYR VAL ALA TRP TYR GLN GLN SEQRES 4 E 216 VAL PRO GLY THR ALA PRO LYS LEU LEU ILE TYR ASP SER SEQRES 5 E 216 ASN LYS ARG PRO SER GLY VAL SER ASP ARG PHE SER GLY SEQRES 6 E 216 SER LYS SER GLY ILE SER ALA SER LEU ALA ILE THR GLY SEQRES 7 E 216 LEU GLN THR GLY ASP GLU ALA ASP TYR TYR CYS GLY VAL SEQRES 8 E 216 TRP ASP THR SER LEU THR ALA TYR ILE PHE GLY ALA GLY SEQRES 9 E 216 THR ARG LEU THR VAL LEU GLY GLN PRO LYS ALA ALA PRO SEQRES 10 E 216 SER VAL THR LEU PHE PRO PRO SER SER GLU GLU LEU GLN SEQRES 11 E 216 ALA ASN LYS ALA THR LEU VAL CYS LEU ILE SER ASP PHE SEQRES 12 E 216 TYR PRO GLY ALA VAL GLU VAL ALA TRP LYS ALA ASP GLY SEQRES 13 E 216 SER ALA VAL ASN ALA GLY VAL GLU THR THR LYS PRO SER SEQRES 14 E 216 LYS GLN SER ASN ASN LYS TYR ALA ALA SER SER TYR LEU SEQRES 15 E 216 SER LEU THR SER ASP GLN TRP LYS SER HIS LYS SER TYR SEQRES 16 E 216 SER CYS GLN VAL THR HIS GLU GLY SER THR VAL GLU LYS SEQRES 17 E 216 THR VAL ALA PRO ALA GLU CYS SER SEQRES 1 F 8 ALA VAL GLY ILE GLY ALA VAL PHE FORMUL 7 HOH *696(H2 O) HELIX 1 AA1 LEU A 65 SER A 67 5 3 HELIX 2 AA2 THR A 88 THR A 92 5 5 HELIX 3 AA3 SER A 134 SER A 139 1 6 HELIX 4 AA4 SER A 163 SER A 165 5 3 HELIX 5 AA5 SER A 194 GLY A 197 5 4 HELIX 6 AA6 LYS A 208 ASN A 211 5 4 HELIX 7 AA7 GLN B 80 GLU B 84 5 5 HELIX 8 AA8 SER B 125 GLN B 130 1 6 HELIX 9 AA9 SER B 186 SER B 191 1 6 HELIX 10 AB1 LEU D 65 SER D 67 5 3 HELIX 11 AB2 THR D 88 THR D 92 5 5 HELIX 12 AB3 SER D 134 SER D 139 1 6 HELIX 13 AB4 SER D 163 SER D 165 5 3 HELIX 14 AB5 SER D 194 GLY D 197 5 4 HELIX 15 AB6 LYS D 208 ASN D 211 5 4 HELIX 16 AB7 GLN E 80 GLU E 84 5 5 HELIX 17 AB8 SER E 125 GLN E 130 1 6 HELIX 18 AB9 SER E 186 SER E 191 1 6 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 25 N GLN A 3 SHEET 3 AA1 4 GLN A 79 LEU A 84 -1 O LEU A 84 N LEU A 18 SHEET 4 AA1 4 VAL A 69 ASP A 74 -1 N ASP A 74 O GLN A 79 SHEET 1 AA2 6 VAL A 11 MET A 12 0 SHEET 2 AA2 6 VAL A 114 VAL A 118 1 O THR A 117 N MET A 12 SHEET 3 AA2 6 ALA A 93 PRO A 101 -1 N ALA A 93 O VAL A 116 SHEET 4 AA2 6 TYR A 33 GLN A 40 -1 N ILE A 38 O PHE A 96 SHEET 5 AA2 6 LEU A 46 PHE A 53 -1 O ILE A 52 N TRP A 35 SHEET 6 AA2 6 THR A 59 TYR A 61 -1 O TYR A 60 N ILE A 51 SHEET 1 AA3 4 VAL A 11 MET A 12 0 SHEET 2 AA3 4 VAL A 114 VAL A 118 1 O THR A 117 N MET A 12 SHEET 3 AA3 4 ALA A 93 PRO A 101 -1 N ALA A 93 O VAL A 116 SHEET 4 AA3 4 TYR A 109 TRP A 110 -1 O TYR A 109 N GLY A 99 SHEET 1 AA4 4 SER A 127 LEU A 131 0 SHEET 2 AA4 4 THR A 142 TYR A 152 -1 O LEU A 148 N PHE A 129 SHEET 3 AA4 4 TYR A 183 PRO A 192 -1 O VAL A 189 N LEU A 145 SHEET 4 AA4 4 VAL A 170 THR A 172 -1 N HIS A 171 O VAL A 188 SHEET 1 AA5 4 SER A 127 LEU A 131 0 SHEET 2 AA5 4 THR A 142 TYR A 152 -1 O LEU A 148 N PHE A 129 SHEET 3 AA5 4 TYR A 183 PRO A 192 -1 O VAL A 189 N LEU A 145 SHEET 4 AA5 4 VAL A 176 LEU A 177 -1 N VAL A 176 O SER A 184 SHEET 1 AA6 7 THR A 158 TRP A 161 0 SHEET 2 AA6 7 VAL A 202 HIS A 207 -1 O ASN A 206 N THR A 158 SHEET 3 AA6 7 THR A 212 ARG A 217 -1 O THR A 212 N HIS A 207 SHEET 4 AA6 7 SER E 204 VAL E 210 -1 O GLU E 207 N LYS A 213 SHEET 5 AA6 7 TYR E 195 HIS E 201 -1 N HIS E 201 O SER E 204 SHEET 6 AA6 7 GLU E 149 ALA E 154 -1 N GLU E 149 O THR E 200 SHEET 7 AA6 7 SER E 157 VAL E 159 -1 O VAL E 159 N TRP E 152 SHEET 1 AA7 5 SER B 9 ALA B 12 0 SHEET 2 AA7 5 THR B 105 VAL B 109 1 O THR B 108 N VAL B 10 SHEET 3 AA7 5 ALA B 85 ASP B 93 -1 N ALA B 85 O LEU B 107 SHEET 4 AA7 5 ALA B 35 GLN B 39 -1 N GLN B 39 O ASP B 86 SHEET 5 AA7 5 LYS B 46 ILE B 49 -1 O LEU B 48 N TRP B 36 SHEET 1 AA8 4 SER B 9 ALA B 12 0 SHEET 2 AA8 4 THR B 105 VAL B 109 1 O THR B 108 N VAL B 10 SHEET 3 AA8 4 ALA B 85 ASP B 93 -1 N ALA B 85 O LEU B 107 SHEET 4 AA8 4 ALA B 98 PHE B 101 -1 O ILE B 100 N VAL B 91 SHEET 1 AA9 3 VAL B 18 SER B 23 0 SHEET 2 AA9 3 SER B 71 ILE B 76 -1 O LEU B 74 N ILE B 20 SHEET 3 AA9 3 PHE B 63 SER B 68 -1 N SER B 66 O SER B 73 SHEET 1 AB1 4 SER B 118 PHE B 122 0 SHEET 2 AB1 4 LYS B 133 PHE B 143 -1 O LEU B 139 N THR B 120 SHEET 3 AB1 4 TYR B 176 THR B 185 -1 O LEU B 184 N ALA B 134 SHEET 4 AB1 4 VAL B 163 THR B 165 -1 N GLU B 164 O TYR B 181 SHEET 1 AB2 4 SER B 118 PHE B 122 0 SHEET 2 AB2 4 LYS B 133 PHE B 143 -1 O LEU B 139 N THR B 120 SHEET 3 AB2 4 TYR B 176 THR B 185 -1 O LEU B 184 N ALA B 134 SHEET 4 AB2 4 SER B 169 LYS B 170 -1 N SER B 169 O ALA B 177 SHEET 1 AB3 4 SER B 157 VAL B 159 0 SHEET 2 AB3 4 GLU B 149 ALA B 154 -1 N TRP B 152 O VAL B 159 SHEET 3 AB3 4 TYR B 195 HIS B 201 -1 O SER B 196 N LYS B 153 SHEET 4 AB3 4 SER B 204 VAL B 210 -1 O SER B 204 N HIS B 201 SHEET 1 AB4 4 GLN D 3 SER D 7 0 SHEET 2 AB4 4 LEU D 18 SER D 25 -1 O SER D 25 N GLN D 3 SHEET 3 AB4 4 GLN D 79 LEU D 84 -1 O LEU D 84 N LEU D 18 SHEET 4 AB4 4 VAL D 69 ASP D 74 -1 N ASP D 74 O GLN D 79 SHEET 1 AB5 6 VAL D 11 MET D 12 0 SHEET 2 AB5 6 VAL D 114 VAL D 118 1 O THR D 117 N MET D 12 SHEET 3 AB5 6 ALA D 93 PRO D 101 -1 N ALA D 93 O VAL D 116 SHEET 4 AB5 6 TYR D 33 GLN D 40 -1 N ILE D 38 O PHE D 96 SHEET 5 AB5 6 LEU D 46 PHE D 53 -1 O ILE D 52 N TRP D 35 SHEET 6 AB5 6 THR D 59 TYR D 61 -1 O TYR D 60 N ILE D 51 SHEET 1 AB6 4 VAL D 11 MET D 12 0 SHEET 2 AB6 4 VAL D 114 VAL D 118 1 O THR D 117 N MET D 12 SHEET 3 AB6 4 ALA D 93 PRO D 101 -1 N ALA D 93 O VAL D 116 SHEET 4 AB6 4 TYR D 109 TRP D 110 -1 O TYR D 109 N GLY D 99 SHEET 1 AB7 4 SER D 127 LEU D 131 0 SHEET 2 AB7 4 THR D 142 TYR D 152 -1 O LYS D 150 N SER D 127 SHEET 3 AB7 4 TYR D 183 PRO D 192 -1 O LEU D 185 N VAL D 149 SHEET 4 AB7 4 VAL D 170 THR D 172 -1 N HIS D 171 O VAL D 188 SHEET 1 AB8 4 SER D 127 LEU D 131 0 SHEET 2 AB8 4 THR D 142 TYR D 152 -1 O LYS D 150 N SER D 127 SHEET 3 AB8 4 TYR D 183 PRO D 192 -1 O LEU D 185 N VAL D 149 SHEET 4 AB8 4 VAL D 176 LEU D 177 -1 N VAL D 176 O SER D 184 SHEET 1 AB9 3 THR D 158 TRP D 161 0 SHEET 2 AB9 3 VAL D 202 HIS D 207 -1 O ASN D 204 N SER D 160 SHEET 3 AB9 3 THR D 212 ARG D 217 -1 O THR D 212 N HIS D 207 SHEET 1 AC1 5 SER E 9 ALA E 12 0 SHEET 2 AC1 5 THR E 105 VAL E 109 1 O THR E 108 N VAL E 10 SHEET 3 AC1 5 ASP E 86 ASP E 93 -1 N TYR E 87 O THR E 105 SHEET 4 AC1 5 ALA E 35 GLN E 39 -1 N GLN E 39 O ASP E 86 SHEET 5 AC1 5 LYS E 46 ILE E 49 -1 O LEU E 48 N TRP E 36 SHEET 1 AC2 4 SER E 9 ALA E 12 0 SHEET 2 AC2 4 THR E 105 VAL E 109 1 O THR E 108 N VAL E 10 SHEET 3 AC2 4 ASP E 86 ASP E 93 -1 N TYR E 87 O THR E 105 SHEET 4 AC2 4 ALA E 98 PHE E 101 -1 O ALA E 98 N ASP E 93 SHEET 1 AC3 3 VAL E 18 SER E 23 0 SHEET 2 AC3 3 SER E 71 ILE E 76 -1 O LEU E 74 N ILE E 20 SHEET 3 AC3 3 PHE E 63 SER E 68 -1 N SER E 68 O SER E 71 SHEET 1 AC4 4 SER E 118 PHE E 122 0 SHEET 2 AC4 4 LYS E 133 PHE E 143 -1 O SER E 141 N SER E 118 SHEET 3 AC4 4 TYR E 176 THR E 185 -1 O LEU E 184 N ALA E 134 SHEET 4 AC4 4 VAL E 163 THR E 165 -1 N GLU E 164 O TYR E 181 SHEET 1 AC5 4 SER E 118 PHE E 122 0 SHEET 2 AC5 4 LYS E 133 PHE E 143 -1 O SER E 141 N SER E 118 SHEET 3 AC5 4 TYR E 176 THR E 185 -1 O LEU E 184 N ALA E 134 SHEET 4 AC5 4 SER E 169 LYS E 170 -1 N SER E 169 O ALA E 177 SSBOND 1 CYS A 22 CYS A 97 1555 1555 2.12 SSBOND 2 CYS A 147 CYS A 203 1555 1555 2.03 SSBOND 3 CYS B 22 CYS B 89 1555 1555 2.07 SSBOND 4 CYS B 138 CYS B 197 1555 1555 2.04 SSBOND 5 CYS D 22 CYS D 97 1555 1555 2.12 SSBOND 6 CYS D 147 CYS D 203 1555 1555 2.02 SSBOND 7 CYS E 22 CYS E 89 1555 1555 2.07 SSBOND 8 CYS E 138 CYS E 197 1555 1555 2.03 CISPEP 1 PHE A 153 PRO A 154 0 -6.13 CISPEP 2 GLU A 155 PRO A 156 0 -1.49 CISPEP 3 TYR B 144 PRO B 145 0 1.39 CISPEP 4 PHE D 153 PRO D 154 0 -6.23 CISPEP 5 GLU D 155 PRO D 156 0 -0.85 CISPEP 6 TYR E 144 PRO E 145 0 0.89 CRYST1 72.574 52.504 151.716 90.00 90.68 90.00 P 1 21 1 4 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 0.013779 0.000000 0.000163 0.00000 SCALE2 0.000000 0.019046 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006592 0.00000