HEADER TRANSFERASE 30-MAR-14 4P86 TITLE STRUCTURE OF PYRR PROTEIN FROM BACILLUS SUBTILIS WITH GMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL PROTEIN PYRR; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: PYRIMIDINE OPERON REGULATORY PROTEIN PYRR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRSET KEYWDS RNA BINDING PROTEINS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.PERICA,Y.KONDO,S.TIWARI,S.MCLAUGHLIN,A.STEWARD,N.REUTER,J.CLARKE, AUTHOR 2 S.A.TEICHMANN REVDAT 3 31-DEC-14 4P86 1 JRNL REVDAT 2 24-DEC-14 4P86 1 DBREF REVDAT 1 17-DEC-14 4P86 0 JRNL AUTH T.PERICA,Y.KONDO,S.P.TIWARI,S.H.MCLAUGHLIN,K.R.KEMPLEN, JRNL AUTH 2 X.ZHANG,A.STEWARD,N.REUTER,J.CLARKE,S.A.TEICHMANN JRNL TITL EVOLUTION OF OLIGOMERIC STATE THROUGH ALLOSTERIC PATHWAYS JRNL TITL 2 THAT MIMIC LIGAND BINDING. JRNL REF SCIENCE V. 346 54346 2014 JRNL REFN ESSN 1095-9203 JRNL PMID 25525255 JRNL DOI 10.1126/SCIENCE.1254346 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0069 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 50228 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2692 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) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3730 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE SET COUNT : 188 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5477 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 150 REMARK 3 SOLVENT ATOMS : 203 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.32000 REMARK 3 B22 (A**2) : 1.45000 REMARK 3 B33 (A**2) : -0.52000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.31000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.167 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.145 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.087 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5698 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5662 ; 0.011 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7733 ; 1.995 ; 2.020 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12994 ; 1.759 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 694 ; 6.259 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 262 ;37.086 ;24.656 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1058 ;17.206 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 56 ;24.324 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 931 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6284 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1160 ; 0.008 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2797 ; 4.623 ; 4.115 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2796 ; 4.621 ; 4.113 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3484 ; 6.533 ; 6.116 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3485 ; 6.532 ; 6.119 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2901 ; 5.943 ; 4.812 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2901 ; 5.941 ; 4.812 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4250 ; 8.794 ; 6.962 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 23543 ;11.878 ;39.835 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 23543 ;11.878 ;39.835 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 3 180 C 3 180 10459 0.15 0.05 REMARK 3 2 A 4 181 B 4 181 10651 0.14 0.05 REMARK 3 3 A 3 180 D 3 180 11055 0.13 0.05 REMARK 3 4 C 4 179 B 4 179 10363 0.14 0.05 REMARK 3 5 C 3 180 D 3 180 10394 0.16 0.05 REMARK 3 6 B 4 179 D 4 179 10563 0.14 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4P86 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000200911. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50228 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 54.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.33400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: 1A3C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25.5% PEG 4000, 0.085 M NA CITRATE PH REMARK 280 5.6, 0.17 M AMMONIUM ACETATE, 15% GLYCEROL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 48.97000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.76500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 48.97000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.76500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 GLY A 0 REMARK 465 SER A 1 REMARK 465 ASN A 2 REMARK 465 LYS A 78 REMARK 465 LYS A 79 REMARK 465 LYS A 182 REMARK 465 GLY B 0 REMARK 465 SER B 1 REMARK 465 ASN B 2 REMARK 465 GLN B 3 REMARK 465 SER B 77 REMARK 465 LYS B 78 REMARK 465 LYS B 79 REMARK 465 LYS B 182 REMARK 465 GLY C 0 REMARK 465 SER C 1 REMARK 465 ASN C 2 REMARK 465 SER C 77 REMARK 465 LYS C 78 REMARK 465 LYS C 79 REMARK 465 THR C 80 REMARK 465 GLU C 181 REMARK 465 LYS C 182 REMARK 465 GLY D 0 REMARK 465 SER D 1 REMARK 465 ASN D 2 REMARK 465 SER D 77 REMARK 465 LYS D 78 REMARK 465 LYS D 79 REMARK 465 THR D 80 REMARK 465 GLU D 181 REMARK 465 LYS D 182 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 OE2 GLU C 52 NE2 GLN C 56 1.67 REMARK 500 O HOH C 321 O HOH C 342 1.94 REMARK 500 O ALA B 120 OD1 ASP B 123 2.03 REMARK 500 O ASP C 123 NH1 ARG C 126 2.04 REMARK 500 O HOH C 343 O HOH C 359 2.07 REMARK 500 OD1 ASP A 74 N LEU A 76 2.13 REMARK 500 O SER D 159 OD1 ASN D 180 2.14 REMARK 500 NE2 HIS A 22 O2 GOL A 202 2.16 REMARK 500 OD1 ASP A 170 O HOH A 301 2.18 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 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 15 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG A 141 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 141 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG B 15 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG B 15 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 27 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 141 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 GLY C 125 N - CA - C ANGL. DEV. = -15.9 DEGREES REMARK 500 ARG D 15 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG D 15 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG D 141 NE - CZ - NH1 ANGL. DEV. = -7.1 DEGREES REMARK 500 ARG D 141 NE - CZ - NH2 ANGL. DEV. = 3.0 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 LYS A 40 -169.72 63.06 REMARK 500 LEU A 76 -10.81 86.09 REMARK 500 TYR A 109 -100.57 -128.69 REMARK 500 LYS B 40 -173.31 60.88 REMARK 500 ASN B 82 7.50 88.34 REMARK 500 TYR B 109 -97.24 -126.21 REMARK 500 ALA C 5 138.67 -173.69 REMARK 500 MET C 31 7.50 84.22 REMARK 500 LYS C 40 -169.12 61.76 REMARK 500 TYR C 109 -97.17 -132.57 REMARK 500 LYS D 4 140.05 -170.42 REMARK 500 LYS D 40 -169.57 64.20 REMARK 500 TYR D 109 -96.80 -126.78 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 ARG A 73 ASP A 74 40.97 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 5GP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5GP B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5GP B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5GP C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5GP C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5GP D 201 DBREF 4P86 A 0 182 PDB 4P86 4P86 0 182 DBREF 4P86 B 0 182 PDB 4P86 4P86 0 182 DBREF 4P86 C 0 182 PDB 4P86 4P86 0 182 DBREF 4P86 D 0 182 PDB 4P86 4P86 0 182 SEQRES 1 A 183 GLY SER ASN GLN LYS ALA VAL ILE LEU ASP GLU GLN ALA SEQRES 2 A 183 ILE ARG ARG ALA LEU THR ARG ILE ALA HIS GLU MET ILE SEQRES 3 A 183 GLU ARG ASN LYS GLY MET ASN ASN CYS ILE LEU VAL GLY SEQRES 4 A 183 ILE LYS THR ARG GLY ILE TYR LEU ALA LYS ARG LEU ALA SEQRES 5 A 183 GLU ARG ILE GLU GLN ILE GLU GLY ASN PRO VAL THR VAL SEQRES 6 A 183 GLY GLU ILE ASP ILE THR LEU TYR ARG ASP ASP LEU SER SEQRES 7 A 183 LYS LYS THR SER ASN ASP GLU PRO LEU VAL LYS GLY ALA SEQRES 8 A 183 ASP ILE PRO VAL ASP ILE THR ASP GLN LYS VAL ILE LEU SEQRES 9 A 183 VAL ASP ASP VAL LEU TYR THR GLY ARG THR VAL ARG ALA SEQRES 10 A 183 GLY MET ASP ALA LEU VAL ASP VAL GLY ARG PRO SER SER SEQRES 11 A 183 ILE GLN LEU ALA VAL LEU VAL ASP ARG GLY HIS ARG GLU SEQRES 12 A 183 LEU PRO ILE ARG ALA ASP TYR ILE GLY LYS ASN ILE PRO SEQRES 13 A 183 THR SER LYS SER GLU LYS VAL MET VAL GLN LEU ASP GLU SEQRES 14 A 183 VAL ASP GLN ASN ASP LEU VAL ALA ILE TYR GLU ASN GLU SEQRES 15 A 183 LYS SEQRES 1 B 183 GLY SER ASN GLN LYS ALA VAL ILE LEU ASP GLU GLN ALA SEQRES 2 B 183 ILE ARG ARG ALA LEU THR ARG ILE ALA HIS GLU MET ILE SEQRES 3 B 183 GLU ARG ASN LYS GLY MET ASN ASN CYS ILE LEU VAL GLY SEQRES 4 B 183 ILE LYS THR ARG GLY ILE TYR LEU ALA LYS ARG LEU ALA SEQRES 5 B 183 GLU ARG ILE GLU GLN ILE GLU GLY ASN PRO VAL THR VAL SEQRES 6 B 183 GLY GLU ILE ASP ILE THR LEU TYR ARG ASP ASP LEU SER SEQRES 7 B 183 LYS LYS THR SER ASN ASP GLU PRO LEU VAL LYS GLY ALA SEQRES 8 B 183 ASP ILE PRO VAL ASP ILE THR ASP GLN LYS VAL ILE LEU SEQRES 9 B 183 VAL ASP ASP VAL LEU TYR THR GLY ARG THR VAL ARG ALA SEQRES 10 B 183 GLY MET ASP ALA LEU VAL ASP VAL GLY ARG PRO SER SER SEQRES 11 B 183 ILE GLN LEU ALA VAL LEU VAL ASP ARG GLY HIS ARG GLU SEQRES 12 B 183 LEU PRO ILE ARG ALA ASP TYR ILE GLY LYS ASN ILE PRO SEQRES 13 B 183 THR SER LYS SER GLU LYS VAL MET VAL GLN LEU ASP GLU SEQRES 14 B 183 VAL ASP GLN ASN ASP LEU VAL ALA ILE TYR GLU ASN GLU SEQRES 15 B 183 LYS SEQRES 1 C 183 GLY SER ASN GLN LYS ALA VAL ILE LEU ASP GLU GLN ALA SEQRES 2 C 183 ILE ARG ARG ALA LEU THR ARG ILE ALA HIS GLU MET ILE SEQRES 3 C 183 GLU ARG ASN LYS GLY MET ASN ASN CYS ILE LEU VAL GLY SEQRES 4 C 183 ILE LYS THR ARG GLY ILE TYR LEU ALA LYS ARG LEU ALA SEQRES 5 C 183 GLU ARG ILE GLU GLN ILE GLU GLY ASN PRO VAL THR VAL SEQRES 6 C 183 GLY GLU ILE ASP ILE THR LEU TYR ARG ASP ASP LEU SER SEQRES 7 C 183 LYS LYS THR SER ASN ASP GLU PRO LEU VAL LYS GLY ALA SEQRES 8 C 183 ASP ILE PRO VAL ASP ILE THR ASP GLN LYS VAL ILE LEU SEQRES 9 C 183 VAL ASP ASP VAL LEU TYR THR GLY ARG THR VAL ARG ALA SEQRES 10 C 183 GLY MET ASP ALA LEU VAL ASP VAL GLY ARG PRO SER SER SEQRES 11 C 183 ILE GLN LEU ALA VAL LEU VAL ASP ARG GLY HIS ARG GLU SEQRES 12 C 183 LEU PRO ILE ARG ALA ASP TYR ILE GLY LYS ASN ILE PRO SEQRES 13 C 183 THR SER LYS SER GLU LYS VAL MET VAL GLN LEU ASP GLU SEQRES 14 C 183 VAL ASP GLN ASN ASP LEU VAL ALA ILE TYR GLU ASN GLU SEQRES 15 C 183 LYS SEQRES 1 D 183 GLY SER ASN GLN LYS ALA VAL ILE LEU ASP GLU GLN ALA SEQRES 2 D 183 ILE ARG ARG ALA LEU THR ARG ILE ALA HIS GLU MET ILE SEQRES 3 D 183 GLU ARG ASN LYS GLY MET ASN ASN CYS ILE LEU VAL GLY SEQRES 4 D 183 ILE LYS THR ARG GLY ILE TYR LEU ALA LYS ARG LEU ALA SEQRES 5 D 183 GLU ARG ILE GLU GLN ILE GLU GLY ASN PRO VAL THR VAL SEQRES 6 D 183 GLY GLU ILE ASP ILE THR LEU TYR ARG ASP ASP LEU SER SEQRES 7 D 183 LYS LYS THR SER ASN ASP GLU PRO LEU VAL LYS GLY ALA SEQRES 8 D 183 ASP ILE PRO VAL ASP ILE THR ASP GLN LYS VAL ILE LEU SEQRES 9 D 183 VAL ASP ASP VAL LEU TYR THR GLY ARG THR VAL ARG ALA SEQRES 10 D 183 GLY MET ASP ALA LEU VAL ASP VAL GLY ARG PRO SER SER SEQRES 11 D 183 ILE GLN LEU ALA VAL LEU VAL ASP ARG GLY HIS ARG GLU SEQRES 12 D 183 LEU PRO ILE ARG ALA ASP TYR ILE GLY LYS ASN ILE PRO SEQRES 13 D 183 THR SER LYS SER GLU LYS VAL MET VAL GLN LEU ASP GLU SEQRES 14 D 183 VAL ASP GLN ASN ASP LEU VAL ALA ILE TYR GLU ASN GLU SEQRES 15 D 183 LYS HET 5GP A 201 24 HET GOL A 202 6 HET 5GP B 201 24 HET 5GP B 202 24 HET 5GP C 201 24 HET 5GP C 202 24 HET 5GP D 201 24 HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 5GP 6(C10 H14 N5 O8 P) FORMUL 6 GOL C3 H8 O3 FORMUL 12 HOH *203(H2 O) HELIX 1 AA1 ASP A 9 LYS A 29 1 21 HELIX 2 AA2 LYS A 40 GLY A 59 1 20 HELIX 3 AA3 GLY A 111 GLY A 125 1 15 HELIX 4 AA4 LEU A 166 GLN A 171 1 6 HELIX 5 AA5 ASP B 9 LYS B 29 1 21 HELIX 6 AA6 LYS B 40 GLY B 59 1 20 HELIX 7 AA7 GLY B 111 VAL B 122 1 12 HELIX 8 AA8 LEU B 166 GLN B 171 1 6 HELIX 9 AA9 ASP C 9 LYS C 29 1 21 HELIX 10 AB1 LYS C 40 GLY C 59 1 20 HELIX 11 AB2 GLY C 111 GLY C 125 1 15 HELIX 12 AB3 LEU C 166 GLN C 171 1 6 HELIX 13 AB4 ASP D 9 LYS D 29 1 21 HELIX 14 AB5 LYS D 40 GLY D 59 1 20 HELIX 15 AB6 GLY D 111 GLY D 125 1 15 HELIX 16 AB7 LEU D 166 GLN D 171 1 6 SHEET 1 AA1 3 ALA A 5 LEU A 8 0 SHEET 2 AA1 3 LEU A 174 GLU A 179 -1 O VAL A 175 N ILE A 7 SHEET 3 AA1 3 GLU A 160 GLN A 165 -1 N MET A 163 O ALA A 176 SHEET 1 AA2 6 GLU A 84 ASP A 91 0 SHEET 2 AA2 6 THR A 63 TYR A 72 -1 N ASP A 68 O GLY A 89 SHEET 3 AA2 6 CYS A 34 ILE A 39 1 N LEU A 36 O GLY A 65 SHEET 4 AA2 6 LYS A 100 LEU A 108 1 O ILE A 102 N ILE A 35 SHEET 5 AA2 6 SER A 129 ASP A 137 1 O ALA A 133 N LEU A 103 SHEET 6 AA2 6 TYR A 149 ASN A 153 1 O TYR A 149 N VAL A 134 SHEET 1 AA3 3 ALA B 5 LEU B 8 0 SHEET 2 AA3 3 LEU B 174 GLU B 179 -1 O VAL B 175 N ILE B 7 SHEET 3 AA3 3 GLU B 160 GLN B 165 -1 N MET B 163 O ALA B 176 SHEET 1 AA4 6 GLU B 84 ASP B 91 0 SHEET 2 AA4 6 VAL B 64 TYR B 72 -1 N ASP B 68 O GLY B 89 SHEET 3 AA4 6 CYS B 34 ILE B 39 1 N LEU B 36 O GLY B 65 SHEET 4 AA4 6 LYS B 100 LEU B 108 1 O ILE B 102 N ILE B 35 SHEET 5 AA4 6 SER B 129 ASP B 137 1 O GLN B 131 N LEU B 103 SHEET 6 AA4 6 TYR B 149 ASN B 153 1 O TYR B 149 N VAL B 134 SHEET 1 AA5 3 ALA C 5 LEU C 8 0 SHEET 2 AA5 3 LEU C 174 GLU C 179 -1 O ILE C 177 N ALA C 5 SHEET 3 AA5 3 GLU C 160 GLN C 165 -1 N MET C 163 O ALA C 176 SHEET 1 AA6 6 GLU C 84 ASP C 91 0 SHEET 2 AA6 6 VAL C 64 TYR C 72 -1 N GLU C 66 O ASP C 91 SHEET 3 AA6 6 CYS C 34 ILE C 39 1 N LEU C 36 O GLY C 65 SHEET 4 AA6 6 LYS C 100 LEU C 108 1 O ILE C 102 N ILE C 35 SHEET 5 AA6 6 SER C 129 ASP C 137 1 O ALA C 133 N LEU C 103 SHEET 6 AA6 6 TYR C 149 ASN C 153 1 O TYR C 149 N VAL C 134 SHEET 1 AA7 3 LYS D 4 LEU D 8 0 SHEET 2 AA7 3 LEU D 174 GLU D 179 -1 O VAL D 175 N ILE D 7 SHEET 3 AA7 3 GLU D 160 GLN D 165 -1 N MET D 163 O ALA D 176 SHEET 1 AA8 6 GLU D 84 ASP D 91 0 SHEET 2 AA8 6 THR D 63 TYR D 72 -1 N ASP D 68 O GLY D 89 SHEET 3 AA8 6 CYS D 34 ILE D 39 1 N LEU D 36 O GLY D 65 SHEET 4 AA8 6 LYS D 100 LEU D 108 1 O ILE D 102 N ILE D 35 SHEET 5 AA8 6 SER D 129 ASP D 137 1 O ALA D 133 N LEU D 103 SHEET 6 AA8 6 TYR D 149 ASN D 153 1 O TYR D 149 N VAL D 134 CISPEP 1 ASP D 74 ASP D 75 0 -23.38 SITE 1 AC1 17 LYS A 40 ASP A 105 ASP A 106 VAL A 107 SITE 2 AC1 17 TYR A 109 THR A 110 GLY A 111 ARG A 112 SITE 3 AC1 17 THR A 113 ARG A 138 LYS A 161 VAL A 162 SITE 4 AC1 17 HOH A 309 HOH A 312 HOH A 318 HOH A 327 SITE 5 AC1 17 HOH C 305 SITE 1 AC2 7 THR A 18 HIS A 22 ARG A 53 ILE A 57 SITE 2 AC2 7 GLU A 181 HIS C 22 ILE C 57 SITE 1 AC3 14 LYS B 40 ASP B 105 ASP B 106 VAL B 107 SITE 2 AC3 14 TYR B 109 THR B 110 GLY B 111 ARG B 112 SITE 3 AC3 14 THR B 113 ARG B 138 LYS B 161 VAL B 162 SITE 4 AC3 14 HOH B 307 HOH B 330 SITE 1 AC4 15 HIS B 140 PRO B 155 THR B 156 SER B 157 SITE 2 AC4 15 HOH B 309 HOH B 331 LYS C 4 ALA C 5 SITE 3 AC4 15 ILE C 7 LYS C 152 PRO C 155 THR C 156 SITE 4 AC4 15 GLU C 160 ILE C 177 5GP C 201 SITE 1 AC5 14 ILE B 7 LYS B 152 PRO B 155 THR B 156 SITE 2 AC5 14 GLU B 160 5GP B 202 HOH B 310 LYS C 4 SITE 3 AC5 14 HIS C 140 PRO C 155 THR C 156 SER C 157 SITE 4 AC5 14 GLU C 160 HOH C 340 SITE 1 AC6 14 LYS C 40 ASP C 105 ASP C 106 VAL C 107 SITE 2 AC6 14 TYR C 109 THR C 110 GLY C 111 ARG C 112 SITE 3 AC6 14 THR C 113 ARG C 138 VAL C 162 HOH C 318 SITE 4 AC6 14 HOH C 341 HOH C 356 SITE 1 AC7 16 LYS D 40 ASP D 105 ASP D 106 VAL D 107 SITE 2 AC7 16 TYR D 109 THR D 110 GLY D 111 ARG D 112 SITE 3 AC7 16 THR D 113 ARG D 138 LYS D 161 VAL D 162 SITE 4 AC7 16 HOH D 303 HOH D 325 HOH D 328 HOH D 331 CRYST1 97.940 77.530 99.780 90.00 102.05 90.00 C 1 2 1 16 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 0.010210 0.000000 0.002180 0.00000 SCALE2 0.000000 0.012898 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010248 0.00000 MASTER 405 0 7 16 36 0 27 6 0 0 0 60 END