HEADER BIOSYNTHETIC PROTEIN 21-DEC-19 6LKZ TITLE CRYSTAL STRUCTURE OF ISOCITRATE DEHYDROGENASE 1 FROM PHAEODACTYLUM TITLE 2 TRICORNUTUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE; COMPND 3 CHAIN: C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHAEODACTYLUM TRICORNUTUM; SOURCE 3 ORGANISM_TAXID: 2850; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOCITRATE DEHYDROGENASE, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.P.ZHU REVDAT 3 29-NOV-23 6LKZ 1 REMARK REVDAT 2 09-NOV-22 6LKZ 1 JRNL REVDAT 1 23-DEC-20 6LKZ 0 JRNL AUTH S.P.HUANG,L.C.ZHOU,B.WEN,P.WANG,G.P.ZHU JRNL TITL BIOCHEMICAL CHARACTERIZATION AND CRYSTAL STRUCTURE OF A JRNL TITL 2 NOVEL NAD+ -DEPENDENT ISOCITRATE DEHYDROGENASE FROM JRNL TITL 3 PHAEODACTYLUM TRICORNUTUM. JRNL REF INT J MOL SCI V. 21 2020 JRNL REFN ESSN 1422-0067 JRNL PMID 32824636 JRNL DOI 10.3390/IJMS21165915 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 29087 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1441 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.0400 - 6.0300 1.00 2922 165 0.2032 0.2337 REMARK 3 2 6.0300 - 4.7900 1.00 2787 163 0.2147 0.2678 REMARK 3 3 4.7900 - 4.1800 1.00 2808 123 0.1887 0.2547 REMARK 3 4 4.1800 - 3.8000 1.00 2763 141 0.2213 0.2825 REMARK 3 5 3.8000 - 3.5300 1.00 2737 167 0.2421 0.3051 REMARK 3 6 3.5300 - 3.3200 1.00 2753 106 0.2549 0.3072 REMARK 3 7 3.3200 - 3.1500 1.00 2733 156 0.2699 0.3476 REMARK 3 8 3.1500 - 3.0200 1.00 2683 154 0.2939 0.3470 REMARK 3 9 3.0200 - 2.9000 1.00 2749 139 0.2993 0.3774 REMARK 3 10 2.9000 - 2.8000 1.00 2711 127 0.2726 0.3607 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) : 0.465 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.554 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 68.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.52 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 : 0.012 7854 REMARK 3 ANGLE : 1.612 10650 REMARK 3 CHIRALITY : 0.074 1132 REMARK 3 PLANARITY : 0.010 1402 REMARK 3 DIHEDRAL : 8.743 4638 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 : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN 'C' REMARK 3 SELECTION : CHAIN 'D' REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6LKZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1300014994. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.988 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29303 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.46100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 6IXL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM SODIUM CHLORIDE, 100 MM SODIUM REMARK 280 HEPES (PH 7.5), 25% (W/V) PEG 4000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 35.98650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.14750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 64.27400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.14750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.98650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 64.27400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 C 1 REMARK 465 LEU C 2 REMARK 465 SER C 3 REMARK 465 VAL C 4 REMARK 465 LYS C 487 REMARK 465 GLU C 488 REMARK 465 LYS C 489 REMARK 465 GLU C 490 REMARK 465 LYS C 491 REMARK 465 LYS C 492 REMARK 465 PRO C 493 REMARK 465 ASP C 494 REMARK 465 VAL C 495 REMARK 465 MET D 1 REMARK 465 LEU D 2 REMARK 465 SER D 3 REMARK 465 VAL D 4 REMARK 465 LYS D 487 REMARK 465 GLU D 488 REMARK 465 LYS D 489 REMARK 465 GLU D 490 REMARK 465 LYS D 491 REMARK 465 LYS D 492 REMARK 465 PRO D 493 REMARK 465 ASP D 494 REMARK 465 VAL D 495 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 ILE C 466 OD2 ASP C 467 1.45 REMARK 500 CD1 PHE D 465 OD1 ASP D 467 1.48 REMARK 500 CE1 PHE D 465 OD1 ASP D 467 1.94 REMARK 500 ND2 ASN C 461 O PHE C 465 2.15 REMARK 500 O HOH D 511 O HOH D 512 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 NZ LYS C 242 OE1 GLU D 241 1455 1.79 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 C 93 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 LYS C 457 CD - CE - NZ ANGL. DEV. = 20.1 DEGREES REMARK 500 LEU C 484 CA - CB - CG ANGL. DEV. = 31.3 DEGREES REMARK 500 ARG D 150 CG - CD - NE ANGL. DEV. = -18.8 DEGREES REMARK 500 ARG D 150 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG D 200 CG - CD - NE ANGL. DEV. = -13.1 DEGREES REMARK 500 ARG D 200 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 GLN D 246 CA - CB - CG ANGL. DEV. = -15.8 DEGREES REMARK 500 ASP D 363 CB - CG - OD1 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG D 438 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG D 442 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 PHE D 465 CB - CG - CD2 ANGL. DEV. = -7.3 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 ASN C 6 85.29 -158.23 REMARK 500 GLU C 20 -149.22 62.08 REMARK 500 LEU C 40 -94.36 -80.94 REMARK 500 SER C 41 -44.55 60.44 REMARK 500 SER C 49 151.27 -48.19 REMARK 500 ASN C 57 58.60 37.89 REMARK 500 SER C 95 127.44 -36.52 REMARK 500 ASN C 108 -153.39 71.56 REMARK 500 ILE C 110 146.44 177.25 REMARK 500 LEU C 124 -163.49 -128.51 REMARK 500 LYS C 127 -50.66 70.26 REMARK 500 ASN C 189 8.32 -69.07 REMARK 500 LYS C 213 41.24 -107.69 REMARK 500 LEU C 245 37.78 -86.49 REMARK 500 THR C 261 -1.34 -56.81 REMARK 500 ARG C 266 -70.31 -77.52 REMARK 500 ARG C 293 -102.65 37.95 REMARK 500 VAL C 322 64.37 61.67 REMARK 500 LYS C 367 -39.48 -141.76 REMARK 500 TYR C 425 72.61 -112.58 REMARK 500 ASP C 426 -124.88 -101.89 REMARK 500 GLU C 427 -89.01 51.49 REMARK 500 ALA C 428 144.47 135.16 REMARK 500 LEU C 433 -122.96 -118.78 REMARK 500 LYS C 457 -76.14 -99.70 REMARK 500 LYS C 460 -109.37 -67.93 REMARK 500 PHE C 465 55.95 25.82 REMARK 500 PHE C 468 -120.87 50.29 REMARK 500 GLU C 469 -71.49 24.89 REMARK 500 THR C 485 -166.68 -75.24 REMARK 500 GLU D 20 -144.88 66.62 REMARK 500 LEU D 40 -94.24 -81.54 REMARK 500 SER D 41 -41.47 61.51 REMARK 500 ASN D 57 52.73 38.20 REMARK 500 SER D 95 130.45 -38.77 REMARK 500 ASN D 108 -156.34 70.47 REMARK 500 ILE D 110 154.25 174.83 REMARK 500 LEU D 124 -164.74 -128.57 REMARK 500 ASP D 161 0.70 -64.44 REMARK 500 ASN D 189 5.50 -68.31 REMARK 500 LEU D 245 35.25 -86.27 REMARK 500 THR D 261 -1.79 -57.32 REMARK 500 ARG D 293 -81.64 -172.62 REMARK 500 SER D 300 81.33 -150.78 REMARK 500 VAL D 322 65.45 65.22 REMARK 500 LYS D 367 -42.31 -142.78 REMARK 500 ALA D 423 -96.81 55.21 REMARK 500 TYR D 425 61.71 -102.68 REMARK 500 ASP D 426 -141.22 -91.51 REMARK 500 GLU D 427 -108.46 50.54 REMARK 500 REMARK 500 THIS ENTRY HAS 59 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY C 109 ILE C 110 125.59 REMARK 500 GLY D 109 ILE D 110 131.34 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 PHE D 465 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 6LKZ C 1 495 PDB 6LKZ 6LKZ 1 495 DBREF 6LKZ D 1 495 PDB 6LKZ 6LKZ 1 495 SEQRES 1 C 495 MET LEU SER VAL GLU ASN LYS VAL VAL ALA PRO PRO MET SEQRES 2 C 495 VAL TYR ILE ALA GLY GLU GLU MET THR ARG TYR ALA CYS SEQRES 3 C 495 ASP LEU VAL VAL LYS SER TRP LEU GLU PRO TYR PHE ASP SEQRES 4 C 495 LEU SER GLN TRP GLU TYR PHE ASP LEU SER CYS VAL ASN SEQRES 5 C 495 ARG ASP ASN THR ASN ASP GLN VAL LEU ARG ASP ALA VAL SEQRES 6 C 495 THR ALA GLY GLN ARG ILE GLY ALA ILE PHE LYS GLU PRO SEQRES 7 C 495 THR ILE THR PRO SER ALA ILE GLN LYS LYS ALA PHE GLY SEQRES 8 C 495 LEU LYS ASN SER LEU GLY SER PRO ASN GLY ALA MET ARG SEQRES 9 C 495 ALA GLY TRP ASN GLY ILE THR ILE SER ARG ASP THR ILE SEQRES 10 C 495 HIS ILE ASP GLY ILE GLU LEU GLY TYR LYS ARG PRO VAL SEQRES 11 C 495 PHE PHE GLU ARG HIS ALA VAL GLY GLY GLU TYR GLY ALA SEQRES 12 C 495 GLY TRP SER LYS VAL GLY ARG GLY THR LEU LEU THR THR SEQRES 13 C 495 TYR LEU PRO SER ASP GLY ARG ASP PRO PHE VAL VAL ASP SEQRES 14 C 495 LYS ARG ASP LEU THR ASP GLN HIS ASN VAL VAL VAL THR SEQRES 15 C 495 TYR HIS ASN PRO TYR ASP ASN VAL GLU PRO LEU ALA HIS SEQRES 16 C 495 LEU PHE PHE GLN ARG CYS LEU ASP ALA ASN ILE THR PRO SEQRES 17 C 495 TYR VAL VAL THR LYS LYS THR VAL PHE LYS TRP GLN GLU SEQRES 18 C 495 GLY PHE TRP ALA VAL MET LYS ASP VAL PHE ASP GLU HIS SEQRES 19 C 495 TYR LYS SER ARG PHE GLU GLU LYS GLY LEU LEU GLN ALA SEQRES 20 C 495 CYS GLY GLY ASP LEU GLN HIS LEU ILE SER ASP ALA ALA SEQRES 21 C 495 THR MET GLN LEU ILE ARG TRP THR ASP GLY GLY PHE GLY SEQRES 22 C 495 MET ALA ALA HIS ASN TYR ASP GLY ASP MET LEU THR ASP SEQRES 23 C 495 GLN ILE ALA GLN VAL HIS ARG SER PRO GLY PHE ILE THR SEQRES 24 C 495 SER ASN LEU VAL GLY LYS ALA PRO ASP GLY SER LEU ILE SEQRES 25 C 495 LYS GLU PHE GLU ALA SER HIS GLY THR VAL SER ASP LEU SEQRES 26 C 495 TRP ASN ASP HIS LEU ALA GLY LYS GLU THR SER LEU ASN SEQRES 27 C 495 PRO LEU GLY LEU VAL GLU ALA ILE VAL GLY ALA LEU GLN SEQRES 28 C 495 HIS ALA ALA VAL LEU ASP ALA GLU LYS ASN PRO ASP ASP SEQRES 29 C 495 GLU HIS LYS VAL LYS ALA ARG ASP GLN ILE PHE ASN PHE SEQRES 30 C 495 THR THR THR LEU ARG THR ALA MET HIS ASN THR PHE ARG SEQRES 31 C 495 TYR GLY GLN GLY THR ARG ASP MET SER GLY PRO SER GLY SEQRES 32 C 495 TYR THR THR GLU ASP PHE VAL ARG LYS VAL ALA TRP ARG SEQRES 33 C 495 LEU GLN ARG TYR LEU ASP ALA GLN TYR ASP GLU ALA PRO SEQRES 34 C 495 PRO PRO GLN LEU GLY GLU PRO SER ARG LYS LEU ARG ARG SEQRES 35 C 495 ASN TYR ASP ILE ASP GLU GLU ALA ILE ASN GLY LEU PHE SEQRES 36 C 495 GLN LYS TYR ASP LYS ASN GLY ASP GLY PHE ILE ASP PHE SEQRES 37 C 495 GLU GLU PHE THR ARG MET LEU VAL LYS MET ASN LEU ALA SEQRES 38 C 495 PRO LEU LEU THR LYS LYS GLU LYS GLU LYS LYS PRO ASP SEQRES 39 C 495 VAL SEQRES 1 D 495 MET LEU SER VAL GLU ASN LYS VAL VAL ALA PRO PRO MET SEQRES 2 D 495 VAL TYR ILE ALA GLY GLU GLU MET THR ARG TYR ALA CYS SEQRES 3 D 495 ASP LEU VAL VAL LYS SER TRP LEU GLU PRO TYR PHE ASP SEQRES 4 D 495 LEU SER GLN TRP GLU TYR PHE ASP LEU SER CYS VAL ASN SEQRES 5 D 495 ARG ASP ASN THR ASN ASP GLN VAL LEU ARG ASP ALA VAL SEQRES 6 D 495 THR ALA GLY GLN ARG ILE GLY ALA ILE PHE LYS GLU PRO SEQRES 7 D 495 THR ILE THR PRO SER ALA ILE GLN LYS LYS ALA PHE GLY SEQRES 8 D 495 LEU LYS ASN SER LEU GLY SER PRO ASN GLY ALA MET ARG SEQRES 9 D 495 ALA GLY TRP ASN GLY ILE THR ILE SER ARG ASP THR ILE SEQRES 10 D 495 HIS ILE ASP GLY ILE GLU LEU GLY TYR LYS ARG PRO VAL SEQRES 11 D 495 PHE PHE GLU ARG HIS ALA VAL GLY GLY GLU TYR GLY ALA SEQRES 12 D 495 GLY TRP SER LYS VAL GLY ARG GLY THR LEU LEU THR THR SEQRES 13 D 495 TYR LEU PRO SER ASP GLY ARG ASP PRO PHE VAL VAL ASP SEQRES 14 D 495 LYS ARG ASP LEU THR ASP GLN HIS ASN VAL VAL VAL THR SEQRES 15 D 495 TYR HIS ASN PRO TYR ASP ASN VAL GLU PRO LEU ALA HIS SEQRES 16 D 495 LEU PHE PHE GLN ARG CYS LEU ASP ALA ASN ILE THR PRO SEQRES 17 D 495 TYR VAL VAL THR LYS LYS THR VAL PHE LYS TRP GLN GLU SEQRES 18 D 495 GLY PHE TRP ALA VAL MET LYS ASP VAL PHE ASP GLU HIS SEQRES 19 D 495 TYR LYS SER ARG PHE GLU GLU LYS GLY LEU LEU GLN ALA SEQRES 20 D 495 CYS GLY GLY ASP LEU GLN HIS LEU ILE SER ASP ALA ALA SEQRES 21 D 495 THR MET GLN LEU ILE ARG TRP THR ASP GLY GLY PHE GLY SEQRES 22 D 495 MET ALA ALA HIS ASN TYR ASP GLY ASP MET LEU THR ASP SEQRES 23 D 495 GLN ILE ALA GLN VAL HIS ARG SER PRO GLY PHE ILE THR SEQRES 24 D 495 SER ASN LEU VAL GLY LYS ALA PRO ASP GLY SER LEU ILE SEQRES 25 D 495 LYS GLU PHE GLU ALA SER HIS GLY THR VAL SER ASP LEU SEQRES 26 D 495 TRP ASN ASP HIS LEU ALA GLY LYS GLU THR SER LEU ASN SEQRES 27 D 495 PRO LEU GLY LEU VAL GLU ALA ILE VAL GLY ALA LEU GLN SEQRES 28 D 495 HIS ALA ALA VAL LEU ASP ALA GLU LYS ASN PRO ASP ASP SEQRES 29 D 495 GLU HIS LYS VAL LYS ALA ARG ASP GLN ILE PHE ASN PHE SEQRES 30 D 495 THR THR THR LEU ARG THR ALA MET HIS ASN THR PHE ARG SEQRES 31 D 495 TYR GLY GLN GLY THR ARG ASP MET SER GLY PRO SER GLY SEQRES 32 D 495 TYR THR THR GLU ASP PHE VAL ARG LYS VAL ALA TRP ARG SEQRES 33 D 495 LEU GLN ARG TYR LEU ASP ALA GLN TYR ASP GLU ALA PRO SEQRES 34 D 495 PRO PRO GLN LEU GLY GLU PRO SER ARG LYS LEU ARG ARG SEQRES 35 D 495 ASN TYR ASP ILE ASP GLU GLU ALA ILE ASN GLY LEU PHE SEQRES 36 D 495 GLN LYS TYR ASP LYS ASN GLY ASP GLY PHE ILE ASP PHE SEQRES 37 D 495 GLU GLU PHE THR ARG MET LEU VAL LYS MET ASN LEU ALA SEQRES 38 D 495 PRO LEU LEU THR LYS LYS GLU LYS GLU LYS LYS PRO ASP SEQRES 39 D 495 VAL FORMUL 3 HOH *24(H2 O) HELIX 1 AA1 GLU C 19 LEU C 34 1 16 HELIX 2 AA2 SER C 49 THR C 56 1 8 HELIX 3 AA3 ASP C 58 GLY C 72 1 15 HELIX 4 AA4 SER C 83 GLY C 91 1 9 HELIX 5 AA5 PRO C 99 ASN C 108 1 10 HELIX 6 AA6 GLY C 139 ALA C 143 5 5 HELIX 7 AA7 ASN C 189 ASN C 205 1 17 HELIX 8 AA8 PHE C 217 TRP C 219 5 3 HELIX 9 AA9 GLN C 220 TYR C 235 1 16 HELIX 10 AB1 TYR C 235 LYS C 242 1 8 HELIX 11 AB2 SER C 257 TRP C 267 1 11 HELIX 12 AB3 HIS C 277 HIS C 292 1 16 HELIX 13 AB4 SER C 294 ILE C 298 5 5 HELIX 14 AB5 VAL C 322 ALA C 331 1 10 HELIX 15 AB6 PRO C 339 ASN C 361 1 23 HELIX 16 AB7 ASP C 364 HIS C 366 5 3 HELIX 17 AB8 LYS C 367 TYR C 391 1 25 HELIX 18 AB9 THR C 395 GLY C 400 1 6 HELIX 19 AC1 PRO C 401 GLY C 403 5 3 HELIX 20 AC2 THR C 405 LEU C 421 1 17 HELIX 21 AC3 SER C 437 ARG C 441 5 5 HELIX 22 AC4 ASP C 447 LYS C 457 1 11 HELIX 23 AC5 GLU C 469 MET C 478 1 10 HELIX 24 AC6 GLU D 19 LEU D 34 1 16 HELIX 25 AC7 SER D 49 THR D 56 1 8 HELIX 26 AC8 ASP D 58 GLY D 72 1 15 HELIX 27 AC9 SER D 83 GLY D 91 1 9 HELIX 28 AD1 PRO D 99 ASN D 108 1 10 HELIX 29 AD2 GLY D 139 ALA D 143 5 5 HELIX 30 AD3 ASN D 189 ASN D 205 1 17 HELIX 31 AD4 PHE D 217 TRP D 219 5 3 HELIX 32 AD5 GLN D 220 TYR D 235 1 16 HELIX 33 AD6 TYR D 235 LYS D 242 1 8 HELIX 34 AD7 SER D 257 TRP D 267 1 11 HELIX 35 AD8 HIS D 277 ARG D 293 1 17 HELIX 36 AD9 SER D 294 ILE D 298 5 5 HELIX 37 AE1 VAL D 322 ALA D 331 1 10 HELIX 38 AE2 PRO D 339 ASN D 361 1 23 HELIX 39 AE3 ASP D 364 TYR D 391 1 28 HELIX 40 AE4 THR D 395 GLY D 400 1 6 HELIX 41 AE5 THR D 405 LEU D 421 1 17 HELIX 42 AE6 SER D 437 ARG D 441 5 5 HELIX 43 AE7 ASP D 447 TYR D 458 1 12 HELIX 44 AE8 PHE D 468 MET D 478 1 11 SHEET 1 AA1 2 VAL C 8 VAL C 9 0 SHEET 2 AA1 2 PHE C 38 ASP C 39 1 O ASP C 39 N VAL C 8 SHEET 1 AA210 TRP C 43 ASP C 47 0 SHEET 2 AA210 MET C 13 ALA C 17 1 N ALA C 17 O PHE C 46 SHEET 3 AA210 ALA C 73 LYS C 76 1 O PHE C 75 N ILE C 16 SHEET 4 AA210 LEU C 311 GLU C 316 1 O LYS C 313 N ILE C 74 SHEET 5 AA210 SER C 300 LYS C 305 -1 N GLY C 304 O ILE C 312 SHEET 6 AA210 THR C 111 ILE C 112 -1 N ILE C 112 O ASN C 301 SHEET 7 AA210 PHE C 131 ARG C 134 -1 O ARG C 134 N THR C 111 SHEET 8 AA210 PHE C 272 ALA C 276 1 O MET C 274 N GLU C 133 SHEET 9 AA210 THR C 207 THR C 212 1 N VAL C 211 O ALA C 275 SHEET 10 AA210 HIS C 254 ILE C 256 1 O LEU C 255 N VAL C 210 SHEET 1 AA3 4 GLY C 144 VAL C 148 0 SHEET 2 AA3 4 ASN C 178 PRO C 186 -1 O THR C 182 N GLY C 144 SHEET 3 AA3 4 ASN D 178 PRO D 186 -1 O VAL D 181 N TYR C 183 SHEET 4 AA3 4 GLY D 144 VAL D 148 -1 N GLY D 144 O THR D 182 SHEET 1 AA4 4 PHE C 166 LEU C 173 0 SHEET 2 AA4 4 GLY C 151 PRO C 159 -1 N TYR C 157 O PHE C 166 SHEET 3 AA4 4 GLY D 151 PRO D 159 -1 O LEU D 154 N THR C 156 SHEET 4 AA4 4 PHE D 166 LEU D 173 -1 O PHE D 166 N TYR D 157 SHEET 1 AA5 2 VAL D 8 VAL D 9 0 SHEET 2 AA5 2 PHE D 38 ASP D 39 1 O ASP D 39 N VAL D 8 SHEET 1 AA610 TRP D 43 ASP D 47 0 SHEET 2 AA610 MET D 13 ALA D 17 1 N ALA D 17 O PHE D 46 SHEET 3 AA610 ALA D 73 LYS D 76 1 O PHE D 75 N ILE D 16 SHEET 4 AA610 LEU D 311 PHE D 315 1 O PHE D 315 N ILE D 74 SHEET 5 AA610 ASN D 301 LYS D 305 -1 N GLY D 304 O ILE D 312 SHEET 6 AA610 THR D 111 ILE D 112 -1 N ILE D 112 O ASN D 301 SHEET 7 AA610 PHE D 131 ARG D 134 -1 O ARG D 134 N THR D 111 SHEET 8 AA610 PHE D 272 ALA D 276 1 O MET D 274 N GLU D 133 SHEET 9 AA610 THR D 207 THR D 212 1 N VAL D 211 O ALA D 275 SHEET 10 AA610 GLN D 253 ILE D 256 1 O LEU D 255 N VAL D 210 CRYST1 71.973 128.548 124.295 90.00 90.00 90.00 P 21 21 21 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 0.013894 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007779 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008045 0.00000