HEADER TRANSFERASE 25-MAY-16 5B69 OBSLTE 03-APR-19 5B69 6JO3 TITLE CRYSTAL STRUCTURE OF GERANYLGERANYLGLYCERYL PHOSPHATE SYNTHASE TITLE 2 COMPLEXED WITH AN G-1-P FROM THERMOPLASMA ACIDOPHILUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: GERANYLGERANYLGLYCERYL PHOSPHATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-246; COMPND 5 SYNONYM: TAGGGPS,(S)-3-O-GERANYLGERANYLGLYCERYL PHOSPHATE SYNTHASE, COMPND 6 PHOSPHOGLYCEROL GERANYLGERANYLTRANSFERASE; COMPND 7 EC: 2.5.1.41; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOPLASMA ACIDOPHILUM (STRAIN ATCC 25905 / SOURCE 3 DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165); SOURCE 4 ORGANISM_TAXID: 273075; SOURCE 5 STRAIN: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165; SOURCE 6 GENE: TA0995; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21C KEYWDS ARCHAEA, ETHER LIPID, THERMOPLASMA, TRANSFERASE, STRUCTURAL GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR N.NEMOTO,K.MIYAZONO,N.KUDO,M.TANOKURA,A.YAMAGISHI REVDAT 3 03-APR-19 5B69 1 OBSLTE REVDAT 2 18-OCT-17 5B69 1 REMARK REVDAT 1 19-JUL-17 5B69 0 JRNL AUTH N.NEMOTO,K.MIYAZONO,N.KUDO,M.TANOKURA,A.YAMAGISHI JRNL TITL CRYSTAL STRUCTURE OF GERANYLGERANYLGLYCERYL PHOSPHATE JRNL TITL 2 SYNTHASE COMPLEXED WITH AN G-1-P FROM THERMOPLASMA JRNL TITL 3 ACIDOPHILUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 30972 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1563 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2138 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE SET COUNT : 111 REMARK 3 BIN FREE R VALUE : 0.4010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3712 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.78000 REMARK 3 B22 (A**2) : 1.78000 REMARK 3 B33 (A**2) : -2.67000 REMARK 3 B12 (A**2) : 0.89000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.282 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.243 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.171 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.380 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3794 ; 0.030 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5126 ; 2.467 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 490 ; 8.589 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 140 ;43.651 ;24.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 674 ;20.497 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;21.936 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 594 ; 0.177 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2770 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1798 ; 0.265 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2603 ; 0.329 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 179 ; 0.183 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 30 ; 0.381 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.294 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2549 ; 1.697 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3936 ; 2.734 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1446 ; 3.927 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1190 ; 5.854 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5B69 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1300000599. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-06; 02-JUL-03 REMARK 200 TEMPERATURE (KELVIN) : 80; 80 REMARK 200 PH : 4.80 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY; SPRING-8 REMARK 200 BEAMLINE : AR-NW12A; BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0; 0.9792 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210; ADSC QUANTUM REMARK 200 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000, HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31121 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.16100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.49700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, 8% PEG 4000, 0.1M REMARK 280 SECIUM CHLORIDE, 0.1M RAC-G1P, PH 4.8, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K, PH 4.80 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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 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 95.00200 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 47.50100 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 71.25150 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 23.75050 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 118.75250 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: 3240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 193 CD GLU A 193 OE2 0.071 REMARK 500 GLU B 104 CB GLU B 104 CG 0.118 REMARK 500 GLU B 104 CG GLU B 104 CD 0.127 REMARK 500 TYR B 129 CD1 TYR B 129 CE1 0.116 REMARK 500 ASN B 232 CB ASN B 232 CG 0.165 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 VAL A 107 CG1 - CB - CG2 ANGL. DEV. = -11.9 DEGREES REMARK 500 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 229 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 MET B 127 CG - SD - CE ANGL. DEV. = -10.8 DEGREES REMARK 500 ARG B 140 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 168 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 205 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 PRO B 239 C - N - CA ANGL. DEV. = -10.3 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 THR A 53 74.92 -62.93 REMARK 500 ASP A 54 -124.00 54.55 REMARK 500 ASP A 56 -151.99 179.90 REMARK 500 SER A 57 -51.89 -147.13 REMARK 500 SER A 81 -70.27 -59.54 REMARK 500 SER A 82 153.51 -43.54 REMARK 500 LEU A 83 77.90 -57.35 REMARK 500 ASN A 99 30.31 -86.43 REMARK 500 VAL A 107 -33.23 -144.81 REMARK 500 PHE A 132 -158.00 -76.99 REMARK 500 MET A 136 -139.66 42.60 REMARK 500 THR A 225 135.89 -39.28 REMARK 500 ILE A 226 -44.90 103.95 REMARK 500 MET B 2 127.85 94.09 REMARK 500 ASP B 54 -96.72 59.84 REMARK 500 ILE B 55 171.60 65.15 REMARK 500 ASP B 56 -102.89 -141.44 REMARK 500 SER B 57 -74.19 -133.66 REMARK 500 ALA B 59 78.32 67.69 REMARK 500 MET B 60 -70.84 153.64 REMARK 500 ALA B 63 -61.38 104.05 REMARK 500 SER B 81 6.74 -68.43 REMARK 500 LEU B 83 3.82 -46.56 REMARK 500 MET B 84 94.55 -55.74 REMARK 500 VAL B 107 -32.51 -147.93 REMARK 500 MET B 136 -140.69 37.88 REMARK 500 PRO B 148 155.72 -46.84 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 ILE A 55 ASP A 56 145.00 REMARK 500 MET A 84 ILE A 85 -147.06 REMARK 500 LYS A 245 GLU A 246 145.46 REMARK 500 SER B 82 LEU B 83 146.43 REMARK 500 LYS B 245 GLU B 246 145.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1GP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1GP B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AF6 RELATED DB: PDB REMARK 900 RELATED ID: 1VIZ RELATED DB: PDB DBREF 5B69 A 1 246 UNP Q9HJH3 GGGPS_THEAC 1 246 DBREF 5B69 B 1 246 UNP Q9HJH3 GGGPS_THEAC 1 246 SEQRES 1 A 246 MET MET THR VAL LEU GLU ASP MET LEU ARG LYS THR ARG SEQRES 2 A 246 ASN GLY LYS VAL HIS MET THR LEU ILE ASP PRO GLY ALA SEQRES 3 A 246 LYS PRO PRO GLN GLU CYS ALA ARG ILE ALA GLU GLU ALA SEQRES 4 A 246 GLU MET ALA GLY THR ASP PHE ILE MET VAL GLY GLY SER SEQRES 5 A 246 THR ASP ILE ASP SER ARG ALA MET ASP GLU ALA ILE SER SEQRES 6 A 246 ALA ILE LYS ALA LYS THR ASP LEU LYS VAL ILE ILE PHE SEQRES 7 A 246 PRO GLY SER SER LEU MET ILE SER PRO LYS ALA ASP ALA SEQRES 8 A 246 ILE PHE PHE MET SER LEU LEU ASN SER GLY SER LEU GLU SEQRES 9 A 246 TYR VAL VAL GLY HIS GLN VAL LYS ALA ALA ILE PRO LEU SEQRES 10 A 246 SER ALA MET LYS ILE GLU LYS ILE PRO MET ALA TYR LEU SEQRES 11 A 246 VAL PHE ASP PRO GLY MET THR VAL GLY ARG VAL GLY LYS SEQRES 12 A 246 ALA HIS LEU ILE PRO ARG ASP ASP GLU LYS THR ALA LEU SEQRES 13 A 246 SER TYR ALA LEU ALA ALA GLN TYR PHE GLY PHE ARG LEU SEQRES 14 A 246 VAL TYR PHE GLU ALA GLY SER GLY SER PRO TYR HIS VAL SEQRES 15 A 246 GLY GLU ASN VAL VAL ARG ARG VAL LYS GLN GLU LEU ASP SEQRES 16 A 246 ILE PRO VAL ILE VAL GLY GLY GLY ILE ARG THR PRO GLU SEQRES 17 A 246 ALA ALA LYS ALA LEU ALA GLN ALA GLY ALA ASP MET ILE SEQRES 18 A 246 VAL THR GLY THR ILE ALA GLU ARG SER VAL ASN VAL TYR SEQRES 19 A 246 GLU ALA LEU HIS PRO ILE VAL GLU SER ILE LYS GLU SEQRES 1 B 246 MET MET THR VAL LEU GLU ASP MET LEU ARG LYS THR ARG SEQRES 2 B 246 ASN GLY LYS VAL HIS MET THR LEU ILE ASP PRO GLY ALA SEQRES 3 B 246 LYS PRO PRO GLN GLU CYS ALA ARG ILE ALA GLU GLU ALA SEQRES 4 B 246 GLU MET ALA GLY THR ASP PHE ILE MET VAL GLY GLY SER SEQRES 5 B 246 THR ASP ILE ASP SER ARG ALA MET ASP GLU ALA ILE SER SEQRES 6 B 246 ALA ILE LYS ALA LYS THR ASP LEU LYS VAL ILE ILE PHE SEQRES 7 B 246 PRO GLY SER SER LEU MET ILE SER PRO LYS ALA ASP ALA SEQRES 8 B 246 ILE PHE PHE MET SER LEU LEU ASN SER GLY SER LEU GLU SEQRES 9 B 246 TYR VAL VAL GLY HIS GLN VAL LYS ALA ALA ILE PRO LEU SEQRES 10 B 246 SER ALA MET LYS ILE GLU LYS ILE PRO MET ALA TYR LEU SEQRES 11 B 246 VAL PHE ASP PRO GLY MET THR VAL GLY ARG VAL GLY LYS SEQRES 12 B 246 ALA HIS LEU ILE PRO ARG ASP ASP GLU LYS THR ALA LEU SEQRES 13 B 246 SER TYR ALA LEU ALA ALA GLN TYR PHE GLY PHE ARG LEU SEQRES 14 B 246 VAL TYR PHE GLU ALA GLY SER GLY SER PRO TYR HIS VAL SEQRES 15 B 246 GLY GLU ASN VAL VAL ARG ARG VAL LYS GLN GLU LEU ASP SEQRES 16 B 246 ILE PRO VAL ILE VAL GLY GLY GLY ILE ARG THR PRO GLU SEQRES 17 B 246 ALA ALA LYS ALA LEU ALA GLN ALA GLY ALA ASP MET ILE SEQRES 18 B 246 VAL THR GLY THR ILE ALA GLU ARG SER VAL ASN VAL TYR SEQRES 19 B 246 GLU ALA LEU HIS PRO ILE VAL GLU SER ILE LYS GLU HET 1GP A 501 10 HET 1GP B 301 10 HETNAM 1GP SN-GLYCEROL-1-PHOSPHATE FORMUL 3 1GP 2(C3 H9 O6 P) FORMUL 5 HOH *88(H2 O) HELIX 1 AA1 THR A 3 GLY A 15 1 13 HELIX 2 AA2 ASP A 23 LYS A 27 5 5 HELIX 3 AA3 PRO A 28 ALA A 42 1 15 HELIX 4 AA4 SER A 57 THR A 71 1 15 HELIX 5 AA5 SER A 102 VAL A 107 1 6 HELIX 6 AA6 VAL A 107 ALA A 119 1 13 HELIX 7 AA7 GLY A 135 GLY A 142 1 8 HELIX 8 AA8 ASP A 151 GLY A 166 1 16 HELIX 9 AA9 GLY A 183 LEU A 194 1 12 HELIX 10 AB1 THR A 206 GLY A 217 1 12 HELIX 11 AB2 ASN A 232 GLU A 246 1 15 HELIX 12 AB3 THR B 3 GLY B 15 1 13 HELIX 13 AB4 ASP B 23 LYS B 27 5 5 HELIX 14 AB5 PRO B 28 GLY B 43 1 16 HELIX 15 AB6 MET B 60 THR B 71 1 12 HELIX 16 AB7 SER B 102 VAL B 107 1 6 HELIX 17 AB8 VAL B 107 ALA B 119 1 13 HELIX 18 AB9 GLY B 135 GLY B 142 1 8 HELIX 19 AC1 ASP B 151 GLY B 166 1 16 HELIX 20 AC2 GLY B 183 LEU B 194 1 12 HELIX 21 AC3 THR B 206 ALA B 216 1 11 HELIX 22 AC4 GLY B 224 ARG B 229 1 6 HELIX 23 AC5 ASN B 232 GLU B 246 1 15 SHEET 1 AA1 9 VAL A 17 ILE A 22 0 SHEET 2 AA1 9 PHE A 46 VAL A 49 1 O MET A 48 N ILE A 22 SHEET 3 AA1 9 LYS A 74 ILE A 77 1 O ILE A 76 N ILE A 47 SHEET 4 AA1 9 ALA A 91 LEU A 97 1 O ALA A 91 N ILE A 77 SHEET 5 AA1 9 GLU A 123 VAL A 131 1 O ILE A 125 N PHE A 94 SHEET 6 AA1 9 LEU A 169 GLU A 173 1 O TYR A 171 N ALA A 128 SHEET 7 AA1 9 VAL A 198 GLY A 201 1 O ILE A 199 N PHE A 172 SHEET 8 AA1 9 MET A 220 THR A 223 1 O VAL A 222 N VAL A 200 SHEET 9 AA1 9 VAL A 17 ILE A 22 1 N MET A 19 O ILE A 221 SHEET 1 AA2 9 VAL B 17 ILE B 22 0 SHEET 2 AA2 9 PHE B 46 VAL B 49 1 O MET B 48 N ILE B 22 SHEET 3 AA2 9 VAL B 75 ILE B 77 1 O ILE B 76 N ILE B 47 SHEET 4 AA2 9 ALA B 91 LEU B 97 1 O PHE B 93 N ILE B 77 SHEET 5 AA2 9 GLU B 123 VAL B 131 1 O ILE B 125 N PHE B 94 SHEET 6 AA2 9 LEU B 169 GLU B 173 1 O TYR B 171 N ALA B 128 SHEET 7 AA2 9 VAL B 198 GLY B 201 1 O ILE B 199 N PHE B 172 SHEET 8 AA2 9 MET B 220 THR B 223 1 O VAL B 222 N VAL B 200 SHEET 9 AA2 9 VAL B 17 ILE B 22 1 N MET B 19 O ILE B 221 CISPEP 1 ASP A 133 PRO A 134 0 9.55 CISPEP 2 ASP B 133 PRO B 134 0 -1.26 SITE 1 AC1 13 LEU A 21 PHE A 78 TYR A 171 GLU A 173 SITE 2 AC1 13 SER A 176 GLY A 177 GLY A 201 GLY A 202 SITE 3 AC1 13 GLY A 203 GLY A 224 THR A 225 HOH A 602 SITE 4 AC1 13 HOH A 609 SITE 1 AC2 15 LEU B 21 PHE B 78 TYR B 171 GLU B 173 SITE 2 AC2 15 SER B 176 GLY B 177 GLY B 201 GLY B 202 SITE 3 AC2 15 GLY B 203 THR B 223 GLY B 224 THR B 225 SITE 4 AC2 15 HOH B 403 HOH B 406 HOH B 414 CRYST1 105.644 105.644 142.503 90.00 90.00 120.00 P 65 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 0.009466 0.005465 0.000000 0.00000 SCALE2 0.000000 0.010930 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007017 0.00000