HEADER MEMBRANE PROTEIN 29-JAN-18 6C9W TITLE CRYSTAL STRUCTURE OF A LIGAND BOUND LACY/NANOBODY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: LACTOSE PERMEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FULL; COMPND 5 SYNONYM: LACTOSE-PROTON SYMPORT; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: NANOBODY9047; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: FULL; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: LACY, B0343, JW0334; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C41; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7-5; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 13 ORGANISM_TAXID: 9844; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: WK6; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PMESY4 KEYWDS MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.KUMAR,J.S.FINER-MOORE,X.JIANG,I.SMIRNOVA,V.KASHO,E.PARDON, AUTHOR 2 J.STEYAERT,H.R.KABACK,R.M.STROUD REVDAT 7 04-OCT-23 6C9W 1 HETSYN REVDAT 6 29-JUL-20 6C9W 1 COMPND REMARK HETNAM SITE REVDAT 6 2 1 ATOM REVDAT 5 01-JAN-20 6C9W 1 REMARK REVDAT 4 20-FEB-19 6C9W 1 REMARK REVDAT 3 05-SEP-18 6C9W 1 JRNL REVDAT 2 29-AUG-18 6C9W 1 JRNL REVDAT 1 15-AUG-18 6C9W 0 JRNL AUTH H.KUMAR,J.S.FINER-MOORE,X.JIANG,I.SMIRNOVA,V.KASHO,E.PARDON, JRNL AUTH 2 J.STEYAERT,H.R.KABACK,R.M.STROUD JRNL TITL CRYSTAL STRUCTURE OF A LIGAND-BOUND LACY-NANOBODY COMPLEX. JRNL REF PROC. NATL. ACAD. SCI. V. 115 8769 2018 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 30108145 JRNL DOI 10.1073/PNAS.1801774115 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 27009 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.277 REMARK 3 R VALUE (WORKING SET) : 0.276 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.670 REMARK 3 FREE R VALUE TEST SET COUNT : 1802 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 29.7583 - 7.0254 1.00 2103 202 0.2356 0.2302 REMARK 3 2 7.0254 - 5.5883 1.00 2089 101 0.2696 0.3048 REMARK 3 3 5.5883 - 4.8854 1.00 2045 101 0.2376 0.2546 REMARK 3 4 4.8854 - 4.4403 1.00 1924 202 0.2212 0.2506 REMARK 3 5 4.4403 - 4.1230 1.00 2002 101 0.2457 0.3537 REMARK 3 6 4.1230 - 3.8804 1.00 1913 202 0.2845 0.3327 REMARK 3 7 3.8804 - 3.6865 1.00 1997 101 0.2985 0.3906 REMARK 3 8 3.6865 - 3.5263 1.00 1987 101 0.3359 0.3370 REMARK 3 9 3.5263 - 3.3907 1.00 1877 202 0.3918 0.3966 REMARK 3 10 3.3907 - 3.2739 1.00 1980 101 0.4055 0.4251 REMARK 3 11 3.2739 - 3.1716 1.00 1966 100 0.4344 0.4327 REMARK 3 12 3.1716 - 3.0810 0.97 1806 199 0.4961 0.4888 REMARK 3 13 3.0810 - 3.0000 0.77 1518 89 0.5595 0.5407 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) : 0.630 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 111.9 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 126.6 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 : 0.005 4252 REMARK 3 ANGLE : 0.725 5761 REMARK 3 CHIRALITY : 0.043 637 REMARK 3 PLANARITY : 0.009 708 REMARK 3 DIHEDRAL : 16.830 1428 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 6C9W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000232271. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1150 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL SI (111) REMARK 200 OPTICS : SN: 926 REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27589 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 29.757 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.85 REMARK 200 R MERGE (I) : 0.19500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 12.11 REMARK 200 R MERGE FOR SHELL (I) : 3.88900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.830 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4ZYR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 77.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MGCL2, 28% PEG1000, 0.1 M TRIS REMARK 280 -HCL, PH 8.5, VAPOR DIFFUSION, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 129.12000 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 64.56000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 96.84000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.28000 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 161.40000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 129.12000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 64.56000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 32.28000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 96.84000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 161.40000 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: DIMERIC 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 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 TYR A 2 REMARK 465 ALA A 195 REMARK 465 THR A 196 REMARK 465 VAL A 197 REMARK 465 ALA A 198 REMARK 465 ASN A 199 REMARK 465 ALA A 200 REMARK 465 VAL A 201 REMARK 465 GLY A 202 REMARK 465 ALA A 203 REMARK 465 ASN A 204 REMARK 465 LEU A 409 REMARK 465 ARG A 410 REMARK 465 ARG A 411 REMARK 465 GLN A 412 REMARK 465 VAL A 413 REMARK 465 ASN A 414 REMARK 465 GLU A 415 REMARK 465 VAL A 416 REMARK 465 ALA A 417 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 ASP A 190 CG OD1 OD2 REMARK 470 HIS A 205 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 43 CG CD CE NZ REMARK 470 ARG B 72 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 76 CG CD CE NZ 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 OE1 GLN B 3 H SER B 25 1.46 REMARK 500 O THR A 310 CD ARG B 57 1.97 REMARK 500 OE1 GLN B 3 N SER B 25 2.19 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 OG SER B 17 OD1 ASP B 73 12544 2.07 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 SER A 311 N - CA - CB ANGL. DEV. = 13.4 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 LEU A 4 -156.98 -75.43 REMARK 500 HIS A 35 -63.04 -98.21 REMARK 500 LEU A 70 39.45 -98.51 REMARK 500 LYS A 74 -0.90 87.54 REMARK 500 ILE A 94 -72.65 -113.18 REMARK 500 TYR A 101 -151.39 -74.94 REMARK 500 PHE A 118 -67.94 -122.44 REMARK 500 ASN A 137 70.22 67.09 REMARK 500 ASN A 165 68.42 61.68 REMARK 500 PRO A 192 -152.89 -68.39 REMARK 500 SER A 249 4.45 -69.76 REMARK 500 ALA A 252 -80.01 -78.72 REMARK 500 THR A 310 13.09 -154.67 REMARK 500 SER A 339 -42.32 -169.48 REMARK 500 PHE A 354 -72.76 -84.73 REMARK 500 PHE A 378 -91.71 -47.71 REMARK 500 PRO A 403 -84.44 -57.56 REMARK 500 PHE B 29 48.42 -89.96 REMARK 500 THR B 31 -62.53 77.06 REMARK 500 ASP B 40 -149.01 -95.75 REMARK 500 VAL B 48 -42.55 -130.97 REMARK 500 ALA B 50 146.18 -170.99 REMARK 500 THR B 54 -13.21 71.62 REMARK 500 ARG B 67 -36.54 -142.20 REMARK 500 ALA B 75 -63.75 59.69 REMARK 500 ALA B 92 178.35 174.22 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 B 57 0.22 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 6C9W A 1 417 UNP P02920 LACY_ECOLI 1 417 DBREF 6C9W B 2 126 PDB 6C9W 6C9W 2 126 SEQADV 6C9W TRP A 46 UNP P02920 GLY 46 ENGINEERED MUTATION SEQADV 6C9W TRP A 262 UNP P02920 GLY 262 ENGINEERED MUTATION SEQRES 1 A 417 MET TYR TYR LEU LYS ASN THR ASN PHE TRP MET PHE GLY SEQRES 2 A 417 LEU PHE PHE PHE PHE TYR PHE PHE ILE MET GLY ALA TYR SEQRES 3 A 417 PHE PRO PHE PHE PRO ILE TRP LEU HIS ASP ILE ASN HIS SEQRES 4 A 417 ILE SER LYS SER ASP THR TRP ILE ILE PHE ALA ALA ILE SEQRES 5 A 417 SER LEU PHE SER LEU LEU PHE GLN PRO LEU PHE GLY LEU SEQRES 6 A 417 LEU SER ASP LYS LEU GLY LEU ARG LYS TYR LEU LEU TRP SEQRES 7 A 417 ILE ILE THR GLY MET LEU VAL MET PHE ALA PRO PHE PHE SEQRES 8 A 417 ILE PHE ILE PHE GLY PRO LEU LEU GLN TYR ASN ILE LEU SEQRES 9 A 417 VAL GLY SER ILE VAL GLY GLY ILE TYR LEU GLY PHE CYS SEQRES 10 A 417 PHE ASN ALA GLY ALA PRO ALA VAL GLU ALA PHE ILE GLU SEQRES 11 A 417 LYS VAL SER ARG ARG SER ASN PHE GLU PHE GLY ARG ALA SEQRES 12 A 417 ARG MET PHE GLY CYS VAL GLY TRP ALA LEU CYS ALA SER SEQRES 13 A 417 ILE VAL GLY ILE MET PHE THR ILE ASN ASN GLN PHE VAL SEQRES 14 A 417 PHE TRP LEU GLY SER GLY CYS ALA LEU ILE LEU ALA VAL SEQRES 15 A 417 LEU LEU PHE PHE ALA LYS THR ASP ALA PRO SER SER ALA SEQRES 16 A 417 THR VAL ALA ASN ALA VAL GLY ALA ASN HIS SER ALA PHE SEQRES 17 A 417 SER LEU LYS LEU ALA LEU GLU LEU PHE ARG GLN PRO LYS SEQRES 18 A 417 LEU TRP PHE LEU SER LEU TYR VAL ILE GLY VAL SER CYS SEQRES 19 A 417 THR TYR ASP VAL PHE ASP GLN GLN PHE ALA ASN PHE PHE SEQRES 20 A 417 THR SER PHE PHE ALA THR GLY GLU GLN GLY THR ARG VAL SEQRES 21 A 417 PHE TRP TYR VAL THR THR MET GLY GLU LEU LEU ASN ALA SEQRES 22 A 417 SER ILE MET PHE PHE ALA PRO LEU ILE ILE ASN ARG ILE SEQRES 23 A 417 GLY GLY LYS ASN ALA LEU LEU LEU ALA GLY THR ILE MET SEQRES 24 A 417 SER VAL ARG ILE ILE GLY SER SER PHE ALA THR SER ALA SEQRES 25 A 417 LEU GLU VAL VAL ILE LEU LYS THR LEU HIS MET PHE GLU SEQRES 26 A 417 VAL PRO PHE LEU LEU VAL GLY CYS PHE LYS TYR ILE THR SEQRES 27 A 417 SER GLN PHE GLU VAL ARG PHE SER ALA THR ILE TYR LEU SEQRES 28 A 417 VAL CYS PHE CYS PHE PHE LYS GLN LEU ALA MET ILE PHE SEQRES 29 A 417 MET SER VAL LEU ALA GLY ASN MET TYR GLU SER ILE GLY SEQRES 30 A 417 PHE GLN GLY ALA TYR LEU VAL LEU GLY LEU VAL ALA LEU SEQRES 31 A 417 GLY PHE THR LEU ILE SER VAL PHE THR LEU SER GLY PRO SEQRES 32 A 417 GLY PRO LEU SER LEU LEU ARG ARG GLN VAL ASN GLU VAL SEQRES 33 A 417 ALA SEQRES 1 B 125 VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN ALA SEQRES 2 B 125 GLY ASP SER LEU ARG LEU SER CYS ALA ALA SER GLY GLY SEQRES 3 B 125 THR PHE SER THR PHE ASN MET GLY TRP PHE ARG GLN ASP SEQRES 4 B 125 LEU GLY LYS GLU ARG GLU PHE VAL ALA ALA ILE ARG TRP SEQRES 5 B 125 THR GLY GLY ARG ALA TYR TYR GLY ASP SER VAL LYS GLY SEQRES 6 B 125 ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR VAL SEQRES 7 B 125 TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 B 125 VAL TYR TYR CYS ALA ARG GLN GLY THR ASN GLY GLY GLY SEQRES 9 B 125 TYR SER GLU ALA THR SER TYR ASN TYR TRP GLY GLN GLY SEQRES 10 B 125 THR GLN VAL THR VAL SER SER HIS HET 9PG A 501 36 HET BNG A 502 51 HETNAM 9PG 4-NITROPHENYL ALPHA-D-GALACTOPYRANOSIDE HETNAM BNG NONYL BETA-D-GLUCOPYRANOSIDE HETSYN 9PG 4-NITROPHENYL ALPHA-D-GALACTOSIDE; 4-NITROPHENYL D- HETSYN 2 9PG GALACTOSIDE; 4-NITROPHENYL GALACTOSIDE HETSYN BNG BETA-NONYLGLUCOSIDE; NONYL BETA-D-GLUCOSIDE; NONYL D- HETSYN 2 BNG GLUCOSIDE; NONYL GLUCOSIDE FORMUL 3 9PG C12 H15 N O8 FORMUL 4 BNG C15 H30 O6 HELIX 1 AA1 ASN A 6 GLY A 24 1 19 HELIX 2 AA2 PHE A 29 ASP A 36 1 8 HELIX 3 AA3 ASP A 44 LEU A 70 1 27 HELIX 4 AA4 LYS A 74 VAL A 85 1 12 HELIX 5 AA5 MET A 86 ILE A 94 1 9 HELIX 6 AA6 ILE A 94 TYR A 101 1 8 HELIX 7 AA7 ASN A 102 PHE A 118 1 17 HELIX 8 AA8 ALA A 120 SER A 136 1 17 HELIX 9 AA9 GLU A 139 THR A 163 1 25 HELIX 10 AB1 GLN A 167 ALA A 187 1 21 HELIX 11 AB2 SER A 209 GLU A 215 1 7 HELIX 12 AB3 GLN A 219 SER A 233 1 15 HELIX 13 AB4 SER A 233 GLN A 242 1 10 HELIX 14 AB5 GLN A 242 SER A 249 1 8 HELIX 15 AB6 THR A 253 GLY A 287 1 35 HELIX 16 AB7 GLY A 288 ALA A 309 1 22 HELIX 17 AB8 SER A 311 LEU A 321 1 11 HELIX 18 AB9 LEU A 321 PHE A 341 1 21 HELIX 19 AC1 GLU A 342 ARG A 344 5 3 HELIX 20 AC2 PHE A 345 CYS A 353 1 9 HELIX 21 AC3 PHE A 354 ILE A 376 1 23 HELIX 22 AC4 GLY A 377 LEU A 400 1 24 HELIX 23 AC5 LYS B 87 THR B 91 5 5 HELIX 24 AC6 GLU B 108 THR B 110 5 3 SHEET 1 AA1 4 VAL B 5 SER B 7 0 SHEET 2 AA1 4 LEU B 20 ALA B 23 -1 O SER B 21 N SER B 7 SHEET 3 AA1 4 THR B 78 GLN B 82 -1 O LEU B 81 N LEU B 20 SHEET 4 AA1 4 THR B 69 ASP B 73 -1 N THR B 69 O GLN B 82 SHEET 1 AA2 6 GLY B 10 GLN B 13 0 SHEET 2 AA2 6 THR B 119 SER B 124 1 O THR B 122 N GLY B 10 SHEET 3 AA2 6 ALA B 92 GLN B 99 -1 N ALA B 92 O VAL B 121 SHEET 4 AA2 6 MET B 34 GLN B 39 -1 N PHE B 37 O TYR B 95 SHEET 5 AA2 6 GLU B 46 ILE B 51 -1 O GLU B 46 N ARG B 38 SHEET 6 AA2 6 ALA B 58 TYR B 60 -1 O TYR B 59 N ALA B 50 SHEET 1 AA3 4 GLY B 10 GLN B 13 0 SHEET 2 AA3 4 THR B 119 SER B 124 1 O THR B 122 N GLY B 10 SHEET 3 AA3 4 ALA B 92 GLN B 99 -1 N ALA B 92 O VAL B 121 SHEET 4 AA3 4 TYR B 112 TRP B 115 -1 O TYR B 114 N ARG B 98 SSBOND 1 CYS B 22 CYS B 96 1555 1555 2.03 CRYST1 153.550 153.550 193.680 90.00 90.00 120.00 P 65 2 2 12 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 0.006513 0.003760 0.000000 0.00000 SCALE2 0.000000 0.007520 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005163 0.00000