HEADER MEMBRANE PROTEIN 25-JUN-24 9CDU TITLE CRYSTAL STRUCTURE OF RHOMBOTARGET A-PEPTIDE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHOMBOTARGET A; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RBB_D10 PEPTIDE; COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACINETOBACTER TERRAE; SOURCE 3 ORGANISM_TAXID: 2731247; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630 KEYWDS DE NOVO DESIGN, DEEP LEARNING, CYCLIC PEPTIDE, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,S.RETTIE,A.KANG,G.BHARDWAJ REVDAT 2 10-DEC-25 9CDU 1 JRNL REVDAT 1 02-JUL-25 9CDU 0 JRNL AUTH S.A.RETTIE,D.JUERGENS,V.ADEBOMI,Y.F.BUESO,Q.ZHAO, JRNL AUTH 2 A.N.LEVEILLE,A.LIU,A.K.BERA,J.A.WILMS,A.UFFING,A.KANG, JRNL AUTH 3 E.BRACKENBROUGH,M.LAMB,S.R.GERBEN,A.MURRAY,P.M.LEVINE, JRNL AUTH 4 M.SCHNEIDER,V.VASIREDDY,S.OVCHINNIKOV,O.H.WEIERGRABER, JRNL AUTH 5 D.WILLBOLD,J.A.KRITZER,J.D.MOUGOUS,D.BAKER,F.DIMAIO, JRNL AUTH 6 G.BHARDWAJ JRNL TITL ACCURATE DE NOVO DESIGN OF HIGH-AFFINITY PROTEIN-BINDING JRNL TITL 2 MACROCYCLES USING DEEP LEARNING. JRNL REF NAT.CHEM.BIOL. V. 21 1948 2025 JRNL REFN ESSN 1552-4469 JRNL PMID 40542165 JRNL DOI 10.1038/S41589-025-01929-W REMARK 2 REMARK 2 RESOLUTION. 2.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_5246 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) : 2.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 32541 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.150 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 34.5600 - 6.2700 1.00 2352 155 0.2082 0.2517 REMARK 3 2 6.2700 - 4.9800 1.00 2229 145 0.2191 0.2563 REMARK 3 3 4.9800 - 4.3500 1.00 2203 145 0.1654 0.2079 REMARK 3 4 4.3500 - 3.9600 1.00 2174 142 0.1813 0.2315 REMARK 3 5 3.9600 - 3.6700 1.00 2188 143 0.1966 0.2371 REMARK 3 6 3.6700 - 3.4600 1.00 2170 142 0.1966 0.2565 REMARK 3 7 3.4600 - 3.2800 1.00 2159 142 0.2053 0.2388 REMARK 3 8 3.2800 - 3.1400 1.00 2151 140 0.2222 0.2608 REMARK 3 9 3.1400 - 3.0200 1.00 2179 143 0.2472 0.2745 REMARK 3 10 3.0200 - 2.9200 1.00 2166 142 0.2660 0.3492 REMARK 3 11 2.9200 - 2.8200 1.00 2139 140 0.2802 0.3732 REMARK 3 12 2.8200 - 2.7400 1.00 2168 142 0.2852 0.3169 REMARK 3 13 2.7400 - 2.6700 1.00 2128 139 0.3086 0.3542 REMARK 3 14 2.6700 - 2.6100 1.00 2135 140 0.3198 0.3860 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.354 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.116 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 58.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.34 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 : 0.002 6904 REMARK 3 ANGLE : 0.476 9322 REMARK 3 CHIRALITY : 0.042 1085 REMARK 3 PLANARITY : 0.005 1227 REMARK 3 DIHEDRAL : 14.156 2546 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 2:443 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.017 30.650 8.389 REMARK 3 T TENSOR REMARK 3 T11: 0.3347 T22: 0.3128 REMARK 3 T33: 0.3017 T12: 0.0088 REMARK 3 T13: 0.0565 T23: -0.0258 REMARK 3 L TENSOR REMARK 3 L11: 2.8426 L22: 1.2364 REMARK 3 L33: 1.8185 L12: 0.6019 REMARK 3 L13: 1.3593 L23: 0.8476 REMARK 3 S TENSOR REMARK 3 S11: 0.0449 S12: -0.1009 S13: 0.1239 REMARK 3 S21: 0.0566 S22: -0.1165 S23: 0.1412 REMARK 3 S31: -0.0136 S32: -0.1363 S33: 0.0713 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN B AND RESID 2:14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.128 41.926 17.998 REMARK 3 T TENSOR REMARK 3 T11: 0.8432 T22: 0.6295 REMARK 3 T33: 0.7911 T12: -0.0539 REMARK 3 T13: -0.0075 T23: -0.0357 REMARK 3 L TENSOR REMARK 3 L11: 2.9824 L22: 4.6506 REMARK 3 L33: 3.2582 L12: 3.5846 REMARK 3 L13: 1.2611 L23: 2.4812 REMARK 3 S TENSOR REMARK 3 S11: 0.0114 S12: -0.6617 S13: 0.0815 REMARK 3 S21: -0.4654 S22: -0.5797 S23: 0.2692 REMARK 3 S31: 0.2305 S32: -0.4319 S33: 0.5043 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN C AND RESID 2:14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.231 35.079 -21.579 REMARK 3 T TENSOR REMARK 3 T11: 1.0656 T22: 0.7644 REMARK 3 T33: 0.8771 T12: -0.2736 REMARK 3 T13: -0.2075 T23: 0.2227 REMARK 3 L TENSOR REMARK 3 L11: 4.2919 L22: 5.8403 REMARK 3 L33: 3.8693 L12: 0.0519 REMARK 3 L13: -1.5091 L23: 0.2244 REMARK 3 S TENSOR REMARK 3 S11: -0.4121 S12: -0.1140 S13: 0.2729 REMARK 3 S21: -0.0497 S22: -0.1561 S23: -1.0290 REMARK 3 S31: -0.7105 S32: 0.5579 S33: 0.5146 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN D AND RESID 1:14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.688 5.160 -28.267 REMARK 3 T TENSOR REMARK 3 T11: 1.3025 T22: 1.8695 REMARK 3 T33: 1.4392 T12: -0.2277 REMARK 3 T13: 0.2223 T23: 0.0994 REMARK 3 L TENSOR REMARK 3 L11: 2.1582 L22: 0.9191 REMARK 3 L33: 1.2544 L12: 1.2026 REMARK 3 L13: -0.2219 L23: -0.0984 REMARK 3 S TENSOR REMARK 3 S11: 0.0974 S12: -0.1923 S13: 0.1270 REMARK 3 S21: -0.3313 S22: 0.4982 S23: -0.3852 REMARK 3 S31: -0.4785 S32: 1.0530 S33: -0.5600 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 9CDU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1000285314. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92010 REMARK 200 MONOCHROMATOR : SI(111) DCM REMARK 200 OPTICS : KB BIMORPH MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32591 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.610 REMARK 200 RESOLUTION RANGE LOW (A) : 34.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.15100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 1.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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 (%): 50.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH REMARK 280 8.5 AND 40 % V/V PEG 400, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 51.38900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 84.91850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 51.38900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 84.91850 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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: 1720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 A 1 REMARK 465 THR A 89 REMARK 465 LEU A 90 REMARK 465 LEU A 444 REMARK 465 ASN A 445 REMARK 465 ASP A 446 REMARK 465 ILE A 447 REMARK 465 PHE A 448 REMARK 465 GLU A 449 REMARK 465 ALA A 450 REMARK 465 GLN A 451 REMARK 465 LYS A 452 REMARK 465 ILE A 453 REMARK 465 GLU A 454 REMARK 465 TRP A 455 REMARK 465 HIS A 456 REMARK 465 GLU A 457 REMARK 465 LEU A 458 REMARK 465 GLU A 459 REMARK 465 HIS A 460 REMARK 465 HIS A 461 REMARK 465 HIS A 462 REMARK 465 HIS A 463 REMARK 465 HIS A 464 REMARK 465 HIS A 465 REMARK 465 MET C 1 REMARK 465 ASP C 87 REMARK 465 SER C 88 REMARK 465 THR C 89 REMARK 465 LEU C 90 REMARK 465 VAL C 91 REMARK 465 SER C 390 REMARK 465 TYR C 391 REMARK 465 ASN C 392 REMARK 465 THR C 393 REMARK 465 LEU C 394 REMARK 465 ALA C 395 REMARK 465 SER C 407 REMARK 465 ASP C 408 REMARK 465 GLY C 409 REMARK 465 THR C 410 REMARK 465 SER C 411 REMARK 465 GLY C 443 REMARK 465 LEU C 444 REMARK 465 ASN C 445 REMARK 465 ASP C 446 REMARK 465 ILE C 447 REMARK 465 PHE C 448 REMARK 465 GLU C 449 REMARK 465 ALA C 450 REMARK 465 GLN C 451 REMARK 465 LYS C 452 REMARK 465 ILE C 453 REMARK 465 GLU C 454 REMARK 465 TRP C 455 REMARK 465 HIS C 456 REMARK 465 GLU C 457 REMARK 465 LEU C 458 REMARK 465 GLU C 459 REMARK 465 HIS C 460 REMARK 465 HIS C 461 REMARK 465 HIS C 462 REMARK 465 HIS C 463 REMARK 465 HIS C 464 REMARK 465 HIS C 465 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 N LYS B 1 O GLN B 14 1.94 REMARK 500 N LYS D 1 O GLN D 14 2.06 REMARK 500 OD1 ASN A 17 O HOH A 601 2.14 REMARK 500 OE2 GLU A 440 O HOH A 602 2.16 REMARK 500 OD1 ASN C 17 O HOH C 601 2.17 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 A 14 56.84 -142.47 REMARK 500 ASN A 17 -156.21 -161.96 REMARK 500 GLU A 120 -36.10 73.85 REMARK 500 LYS A 180 -159.69 -81.07 REMARK 500 SER A 181 33.78 -92.08 REMARK 500 PRO A 211 90.25 -59.49 REMARK 500 GLU A 242 48.75 -76.25 REMARK 500 ASN A 334 -59.07 70.45 REMARK 500 ALA A 335 -121.45 58.49 REMARK 500 ILE A 399 -51.26 -134.56 REMARK 500 THR A 410 -143.64 -101.04 REMARK 500 ASP A 421 -167.31 -117.63 REMARK 500 LEU B 2 -59.60 -144.37 REMARK 500 ASN C 17 -152.89 -137.09 REMARK 500 HIS C 48 19.76 56.83 REMARK 500 LYS C 53 -119.16 53.14 REMARK 500 ASP C 94 -167.06 59.54 REMARK 500 GLU C 120 -52.67 66.63 REMARK 500 GLU C 152 -164.45 -124.61 REMARK 500 PRO C 211 85.64 -60.46 REMARK 500 ASP C 240 -129.57 51.94 REMARK 500 ASP C 241 -161.64 55.67 REMARK 500 ASN C 297 40.27 -109.92 REMARK 500 LEU C 305 55.66 -119.59 REMARK 500 LEU C 405 37.92 -91.61 REMARK 500 THR C 428 -165.59 -102.01 REMARK 500 GLU C 432 -21.50 69.90 REMARK 500 LEU D 2 -35.83 -130.49 REMARK 500 TYR D 8 36.75 71.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PG4 A 503 DBREF 9CDU A 1 465 PDB 9CDU 9CDU 1 465 DBREF 9CDU B 1 14 PDB 9CDU 9CDU 1 14 DBREF 9CDU C 1 465 PDB 9CDU 9CDU 1 465 DBREF 9CDU D 1 14 PDB 9CDU 9CDU 1 14 SEQRES 1 A 465 MET GLY ALA ASP ILE GLU VAL THR THR THR ILE ASP GLU SEQRES 2 A 465 ASP VAL ASP ASN THR VAL CYS SER LEU ARG GLU ALA VAL SEQRES 3 A 465 GLU LEU ILE ASN LYS ARG ASN SER SER ASP SER THR VAL SEQRES 4 A 465 VAL ALA SER VAL LYS ASP GLY TYR HIS GLY CYS GLY ASN SEQRES 5 A 465 LYS ASP ALA SER SER ASN ILE ILE LEU GLN ARG ASP LYS SEQRES 6 A 465 GLU TYR THR LEU ASN SER ARG ILE THR ILE THR ALA PRO SEQRES 7 A 465 LEU THR ILE SER THR ALA LYS ASN ASP SER THR LEU VAL SEQRES 8 A 465 ASP THR ASP GLN PRO GLY SER HIS ASN ALA THR ILE LYS SEQRES 9 A 465 MET ALA GLY THR ASP GLN LEU PHE LYS ILE ASP ASP GLU SEQRES 10 A 465 SER VAL GLU LYS ALA SER PHE SER VAL LEU LEU SER ASP SEQRES 11 A 465 LEU ASN LEU GLN GLY ALA GLY ALA ASN SER LYS VAL LEU SEQRES 12 A 465 THR GLY GLY LEU ILE LEU ASN HIS GLU LYS LEU THR ILE SEQRES 13 A 465 GLN ASN SER ARG LEU THR GLY GLY TYR ALA ASN GLN GLY SEQRES 14 A 465 GLY VAL ILE TYR ASN GLN GLY PHE ALA SER LYS SER ASP SEQRES 15 A 465 ARG THR PHE GLY PHE VAL TYR ILE VAL ASN SER LEU ILE SEQRES 16 A 465 GLN ASN ASN LYS ALA ALA GLN GLY GLY VAL ILE TYR SER SEQRES 17 A 465 GLU GLN PRO LEU PHE LEU ILE THR GLN SER VAL ILE ARG SEQRES 18 A 465 ASP ASN GLU VAL SER ASN THR SER GLY SER LEU PHE PHE SEQRES 19 A 465 SER GLN ASP SER PHE ASP ASP GLU SER THR GLY GLU TYR SEQRES 20 A 465 VAL VAL GLN ARG ALA ILE GLY LEU SER ASN SER THR VAL SEQRES 21 A 465 PHE HIS ASN LYS GLY GLY PHE ILE THR ASN VAL ARG ASP SEQRES 22 A 465 GLY MET PHE VAL ASN ASN ILE THR MET ILE LYS ASN ASP SEQRES 23 A 465 LYS GLY LEU PHE LEU GLU ALA PRO GLN GLY ASN ALA SER SEQRES 24 A 465 ILE SER ASN SER ILE LEU VAL GLY ASN THR ILE ASN CYS SEQRES 25 A 465 GLN ALA ASN SER THR ASP LYS ALA ILE ILE GLN SER ASN SEQRES 26 A 465 LEU VAL THR THR GLU CYS ASN ARG ASN ALA SER VAL LYS SEQRES 27 A 465 VAL PRO ASN ILE LEU TYR PRO ALA ASN GLN LYS LEU ILE SEQRES 28 A 465 ALA GLY SER THR ASP GLU GLY VAL CYS ASP VAL ALA SER SEQRES 29 A 465 LYS ASP GLY LEU LEU CYS PRO PHE ASN THR PRO LYS ASP SEQRES 30 A 465 SER PHE LEU GLY PHE PHE LYS PRO ARG LEU LEU GLU SER SEQRES 31 A 465 TYR ASN THR LEU ALA ASP SER LEU ILE ILE ASN LYS GLY SEQRES 32 A 465 ARG LEU TYR SER ASP GLY THR SER VAL GLY LEU ALA SER SEQRES 33 A 465 CYS GLU THR LEU ASP GLN ARG GLY LYS ARG ARG THR GLY SEQRES 34 A 465 TYR ASP GLU LEU CYS ASP LEU GLY ALA ILE GLU TYR ILE SEQRES 35 A 465 GLY LEU ASN ASP ILE PHE GLU ALA GLN LYS ILE GLU TRP SEQRES 36 A 465 HIS GLU LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 14 LYS LEU PHE GLY PRO ASP PRO TYR LEU PRO GLU ASN VAL SEQRES 2 B 14 GLN SEQRES 1 C 465 MET GLY ALA ASP ILE GLU VAL THR THR THR ILE ASP GLU SEQRES 2 C 465 ASP VAL ASP ASN THR VAL CYS SER LEU ARG GLU ALA VAL SEQRES 3 C 465 GLU LEU ILE ASN LYS ARG ASN SER SER ASP SER THR VAL SEQRES 4 C 465 VAL ALA SER VAL LYS ASP GLY TYR HIS GLY CYS GLY ASN SEQRES 5 C 465 LYS ASP ALA SER SER ASN ILE ILE LEU GLN ARG ASP LYS SEQRES 6 C 465 GLU TYR THR LEU ASN SER ARG ILE THR ILE THR ALA PRO SEQRES 7 C 465 LEU THR ILE SER THR ALA LYS ASN ASP SER THR LEU VAL SEQRES 8 C 465 ASP THR ASP GLN PRO GLY SER HIS ASN ALA THR ILE LYS SEQRES 9 C 465 MET ALA GLY THR ASP GLN LEU PHE LYS ILE ASP ASP GLU SEQRES 10 C 465 SER VAL GLU LYS ALA SER PHE SER VAL LEU LEU SER ASP SEQRES 11 C 465 LEU ASN LEU GLN GLY ALA GLY ALA ASN SER LYS VAL LEU SEQRES 12 C 465 THR GLY GLY LEU ILE LEU ASN HIS GLU LYS LEU THR ILE SEQRES 13 C 465 GLN ASN SER ARG LEU THR GLY GLY TYR ALA ASN GLN GLY SEQRES 14 C 465 GLY VAL ILE TYR ASN GLN GLY PHE ALA SER LYS SER ASP SEQRES 15 C 465 ARG THR PHE GLY PHE VAL TYR ILE VAL ASN SER LEU ILE SEQRES 16 C 465 GLN ASN ASN LYS ALA ALA GLN GLY GLY VAL ILE TYR SER SEQRES 17 C 465 GLU GLN PRO LEU PHE LEU ILE THR GLN SER VAL ILE ARG SEQRES 18 C 465 ASP ASN GLU VAL SER ASN THR SER GLY SER LEU PHE PHE SEQRES 19 C 465 SER GLN ASP SER PHE ASP ASP GLU SER THR GLY GLU TYR SEQRES 20 C 465 VAL VAL GLN ARG ALA ILE GLY LEU SER ASN SER THR VAL SEQRES 21 C 465 PHE HIS ASN LYS GLY GLY PHE ILE THR ASN VAL ARG ASP SEQRES 22 C 465 GLY MET PHE VAL ASN ASN ILE THR MET ILE LYS ASN ASP SEQRES 23 C 465 LYS GLY LEU PHE LEU GLU ALA PRO GLN GLY ASN ALA SER SEQRES 24 C 465 ILE SER ASN SER ILE LEU VAL GLY ASN THR ILE ASN CYS SEQRES 25 C 465 GLN ALA ASN SER THR ASP LYS ALA ILE ILE GLN SER ASN SEQRES 26 C 465 LEU VAL THR THR GLU CYS ASN ARG ASN ALA SER VAL LYS SEQRES 27 C 465 VAL PRO ASN ILE LEU TYR PRO ALA ASN GLN LYS LEU ILE SEQRES 28 C 465 ALA GLY SER THR ASP GLU GLY VAL CYS ASP VAL ALA SER SEQRES 29 C 465 LYS ASP GLY LEU LEU CYS PRO PHE ASN THR PRO LYS ASP SEQRES 30 C 465 SER PHE LEU GLY PHE PHE LYS PRO ARG LEU LEU GLU SER SEQRES 31 C 465 TYR ASN THR LEU ALA ASP SER LEU ILE ILE ASN LYS GLY SEQRES 32 C 465 ARG LEU TYR SER ASP GLY THR SER VAL GLY LEU ALA SER SEQRES 33 C 465 CYS GLU THR LEU ASP GLN ARG GLY LYS ARG ARG THR GLY SEQRES 34 C 465 TYR ASP GLU LEU CYS ASP LEU GLY ALA ILE GLU TYR ILE SEQRES 35 C 465 GLY LEU ASN ASP ILE PHE GLU ALA GLN LYS ILE GLU TRP SEQRES 36 C 465 HIS GLU LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 D 14 LYS LEU PHE GLY PRO ASP PRO TYR LEU PRO GLU ASN VAL SEQRES 2 D 14 GLN HET PG4 A 501 13 HET PG4 A 502 13 HET PG4 A 503 10 HET PG4 C 501 13 HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 5 PG4 4(C8 H18 O5) FORMUL 9 HOH *77(H2 O) HELIX 1 AA1 SER A 21 ASN A 33 1 13 HELIX 2 AA2 ASP A 36 VAL A 43 1 8 HELIX 3 AA3 ALA A 136 SER A 140 5 5 HELIX 4 AA4 SER A 243 GLN A 250 1 8 HELIX 5 AA5 THR A 329 ASN A 332 5 4 HELIX 6 AA6 THR A 393 SER A 397 5 5 HELIX 7 AA7 VAL A 412 SER A 416 5 5 HELIX 8 AA8 SER C 21 ASN C 33 1 13 HELIX 9 AA9 ASP C 36 ALA C 41 1 6 HELIX 10 AB1 ALA C 136 SER C 140 5 5 HELIX 11 AB2 SER C 243 ARG C 251 1 9 HELIX 12 AB3 THR C 329 ASN C 332 5 4 SHEET 1 AA111 ILE A 5 GLU A 6 0 SHEET 2 AA111 ASN A 58 LEU A 61 1 O ILE A 60 N ILE A 5 SHEET 3 AA111 LEU A 79 THR A 83 1 O THR A 80 N ILE A 59 SHEET 4 AA111 SER A 125 SER A 129 1 O LEU A 127 N ILE A 81 SHEET 5 AA111 LYS A 153 GLN A 157 1 O THR A 155 N LEU A 128 SHEET 6 AA111 PHE A 187 VAL A 191 1 O PHE A 187 N LEU A 154 SHEET 7 AA111 PHE A 213 THR A 216 1 O THR A 216 N ILE A 190 SHEET 8 AA111 GLY A 254 SER A 256 1 O GLY A 254 N ILE A 215 SHEET 9 AA111 PHE A 276 ASN A 278 1 O ASN A 278 N LEU A 255 SHEET 10 AA111 SER A 299 SER A 301 1 O SER A 301 N VAL A 277 SHEET 11 AA111 ILE A 321 GLN A 323 1 O ILE A 321 N ILE A 300 SHEET 1 AA2 7 GLU A 66 LEU A 69 0 SHEET 2 AA2 7 ALA A 101 MET A 105 1 O THR A 102 N TYR A 67 SHEET 3 AA2 7 LEU A 131 GLN A 134 1 O ASN A 132 N ILE A 103 SHEET 4 AA2 7 ARG A 160 THR A 162 1 O ARG A 160 N LEU A 133 SHEET 5 AA2 7 LEU A 194 GLN A 202 1 O LEU A 194 N LEU A 161 SHEET 6 AA2 7 VAL A 219 VAL A 225 1 O VAL A 219 N ILE A 195 SHEET 7 AA2 7 LYS A 264 GLY A 265 1 O LYS A 264 N ASN A 223 SHEET 1 AA3 5 TYR A 165 GLN A 168 0 SHEET 2 AA3 5 LEU A 194 GLN A 202 1 O GLN A 202 N ASN A 167 SHEET 3 AA3 5 VAL A 219 VAL A 225 1 O VAL A 219 N ILE A 195 SHEET 4 AA3 5 THR A 259 PHE A 261 1 O THR A 259 N ILE A 220 SHEET 5 AA3 5 THR A 281 MET A 282 1 O THR A 281 N VAL A 260 SHEET 1 AA4 9 ILE A 73 ILE A 75 0 SHEET 2 AA4 9 PHE A 112 ILE A 114 1 O LYS A 113 N ILE A 75 SHEET 3 AA4 9 ILE A 148 ASN A 150 1 O LEU A 149 N ILE A 114 SHEET 4 AA4 9 ILE A 172 ASN A 174 1 O TYR A 173 N ASN A 150 SHEET 5 AA4 9 ILE A 206 SER A 208 1 O TYR A 207 N ASN A 174 SHEET 6 AA4 9 SER A 231 SER A 235 1 O PHE A 234 N SER A 208 SHEET 7 AA4 9 PHE A 267 VAL A 271 1 O ILE A 268 N PHE A 233 SHEET 8 AA4 9 LYS A 287 LEU A 291 1 O GLY A 288 N ILE A 268 SHEET 9 AA4 9 ILE A 310 ALA A 314 1 O GLN A 313 N LEU A 291 SHEET 1 AA5 3 ILE A 304 LEU A 305 0 SHEET 2 AA5 3 LEU A 326 VAL A 327 1 O LEU A 326 N LEU A 305 SHEET 3 AA5 3 ILE A 342 LEU A 343 1 O ILE A 342 N VAL A 327 SHEET 1 AA6 2 GLY A 403 ARG A 404 0 SHEET 2 AA6 2 LEU A 433 CYS A 434 -1 O CYS A 434 N GLY A 403 SHEET 1 AA711 ILE C 5 GLU C 6 0 SHEET 2 AA711 ASN C 58 LEU C 61 1 O ILE C 60 N ILE C 5 SHEET 3 AA711 THR C 80 THR C 83 1 O THR C 80 N ILE C 59 SHEET 4 AA711 SER C 125 SER C 129 1 O SER C 129 N ILE C 81 SHEET 5 AA711 LYS C 153 GLN C 157 1 O THR C 155 N LEU C 128 SHEET 6 AA711 PHE C 187 VAL C 191 1 O TYR C 189 N ILE C 156 SHEET 7 AA711 PHE C 213 THR C 216 1 O THR C 216 N ILE C 190 SHEET 8 AA711 GLY C 254 SER C 256 1 O GLY C 254 N ILE C 215 SHEET 9 AA711 PHE C 276 ASN C 278 1 O ASN C 278 N LEU C 255 SHEET 10 AA711 SER C 299 SER C 301 1 O SER C 301 N VAL C 277 SHEET 11 AA711 ILE C 321 GLN C 323 1 O ILE C 321 N ILE C 300 SHEET 1 AA8 8 GLU C 66 LEU C 69 0 SHEET 2 AA8 8 ALA C 101 MET C 105 1 O THR C 102 N TYR C 67 SHEET 3 AA8 8 LEU C 131 GLN C 134 1 O GLN C 134 N ILE C 103 SHEET 4 AA8 8 ARG C 160 THR C 162 1 O ARG C 160 N LEU C 133 SHEET 5 AA8 8 LEU C 194 GLN C 196 1 O LEU C 194 N LEU C 161 SHEET 6 AA8 8 VAL C 219 ARG C 221 1 O VAL C 219 N ILE C 195 SHEET 7 AA8 8 THR C 259 PHE C 261 1 O THR C 259 N ILE C 220 SHEET 8 AA8 8 THR C 281 MET C 282 1 O THR C 281 N VAL C 260 SHEET 1 AA9 9 ILE C 73 ILE C 75 0 SHEET 2 AA9 9 PHE C 112 ILE C 114 1 O LYS C 113 N ILE C 75 SHEET 3 AA9 9 ILE C 148 ASN C 150 1 O LEU C 149 N ILE C 114 SHEET 4 AA9 9 ILE C 172 ASN C 174 1 O TYR C 173 N ILE C 148 SHEET 5 AA9 9 ILE C 206 SER C 208 1 O TYR C 207 N ASN C 174 SHEET 6 AA9 9 SER C 231 SER C 235 1 O PHE C 234 N SER C 208 SHEET 7 AA9 9 PHE C 267 VAL C 271 1 O ILE C 268 N PHE C 233 SHEET 8 AA9 9 LYS C 287 LEU C 291 1 O GLY C 288 N ILE C 268 SHEET 9 AA9 9 ILE C 310 ALA C 314 1 O ILE C 310 N GLY C 288 SHEET 1 AB1 4 TYR C 165 GLN C 168 0 SHEET 2 AB1 4 LYS C 199 GLN C 202 1 O GLN C 202 N ASN C 167 SHEET 3 AB1 4 GLU C 224 VAL C 225 1 O GLU C 224 N ALA C 200 SHEET 4 AB1 4 LYS C 264 GLY C 265 1 O LYS C 264 N VAL C 225 SHEET 1 AB2 3 ILE C 304 LEU C 305 0 SHEET 2 AB2 3 LEU C 326 VAL C 327 1 O LEU C 326 N LEU C 305 SHEET 3 AB2 3 ILE C 342 LEU C 343 1 O ILE C 342 N VAL C 327 SHEET 1 AB3 2 GLY C 403 ARG C 404 0 SHEET 2 AB3 2 LEU C 433 CYS C 434 -1 O CYS C 434 N GLY C 403 SSBOND 1 CYS A 20 CYS A 50 1555 1555 2.03 SSBOND 2 CYS A 312 CYS A 331 1555 1555 2.03 SSBOND 3 CYS A 360 CYS A 370 1555 1555 2.03 SSBOND 4 CYS A 417 CYS A 434 1555 1555 2.03 SSBOND 5 CYS C 20 CYS C 50 1555 1555 2.03 SSBOND 6 CYS C 312 CYS C 331 1555 1555 2.03 SSBOND 7 CYS C 360 CYS C 370 1555 1555 2.03 SSBOND 8 CYS C 417 CYS C 434 1555 1555 2.03 LINK N LYS B 1 C GLN B 14 1555 1555 1.35 LINK N LYS D 1 C GLN D 14 1555 1555 1.35 CRYST1 102.778 169.837 59.470 90.00 90.00 90.00 P 21 21 2 8 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 0.009730 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005888 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016815 0.00000 CONECT 138 363 CONECT 363 138 CONECT 2331 2471 CONECT 2471 2331 CONECT 2685 2754 CONECT 2754 2685 CONECT 3117 3258 CONECT 3258 3117 CONECT 3326 3433 CONECT 3433 3326 CONECT 3578 3803 CONECT 3803 3578 CONECT 5750 5890 CONECT 5890 5750 CONECT 6104 6173 CONECT 6173 6104 CONECT 6459 6600 CONECT 6600 6459 CONECT 6664 6771 CONECT 6771 6664 CONECT 6779 6780 CONECT 6780 6779 6781 CONECT 6781 6780 6782 CONECT 6782 6781 6783 CONECT 6783 6782 6784 CONECT 6784 6783 6785 CONECT 6785 6784 6786 CONECT 6786 6785 6787 CONECT 6787 6786 6788 CONECT 6788 6787 6789 CONECT 6789 6788 6790 CONECT 6790 6789 6791 CONECT 6791 6790 CONECT 6792 6793 CONECT 6793 6792 6794 CONECT 6794 6793 6795 CONECT 6795 6794 6796 CONECT 6796 6795 6797 CONECT 6797 6796 6798 CONECT 6798 6797 6799 CONECT 6799 6798 6800 CONECT 6800 6799 6801 CONECT 6801 6800 6802 CONECT 6802 6801 6803 CONECT 6803 6802 6804 CONECT 6804 6803 CONECT 6805 6806 CONECT 6806 6805 6807 CONECT 6807 6806 6808 CONECT 6808 6807 6809 CONECT 6809 6808 6810 CONECT 6810 6809 6811 CONECT 6811 6810 6812 CONECT 6812 6811 6813 CONECT 6813 6812 6814 CONECT 6814 6813 CONECT 6815 6816 CONECT 6816 6815 6817 CONECT 6817 6816 6818 CONECT 6818 6817 6819 CONECT 6819 6818 6820 CONECT 6820 6819 6821 CONECT 6821 6820 6822 CONECT 6822 6821 6823 CONECT 6823 6822 6824 CONECT 6824 6823 6825 CONECT 6825 6824 6826 CONECT 6826 6825 6827 CONECT 6827 6826 MASTER 417 0 4 12 74 0 0 6 6900 4 69 76 END