HEADER FLUORESCENT PROTEIN 29-APR-13 4KGF TITLE CRYSTAL STRUCTURE OF NEAR-INFRARED FLUORESCENT PROTEIN WITH AN TITLE 2 EXTENDED STOKES SHIFT, PH 8.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAGRFP675, RED FLUORESCENT PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_COMMON: ARTIFICIAL GENE; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: LMG194; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBAD/HIS-B KEYWDS STRUCTURAL GENOMICS, PROTEINSTRUCTURE INITIATIVE, NEW YORK STRUCTURAL KEYWDS 2 GENOMIX RESEARCHCONSORTIUM, HYDROLASE, PSI-BIOLOGY, NEW YORK KEYWDS 3 STRUCTURAL GENOMICS RESEARCH CONSORTIUM, NYSGRC, FLUORESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.N.MALASHKEVICH,K.PIATKEVICH,S.C.ALMO,V.VERKHUSHA,NEW YORK AUTHOR 2 STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NYSGRC) REVDAT 5 06-DEC-23 4KGF 1 REMARK REVDAT 4 20-SEP-23 4KGF 1 REMARK LINK REVDAT 3 24-JAN-18 4KGF 1 AUTHOR REVDAT 2 08-JAN-14 4KGF 1 JRNL REVDAT 1 08-MAY-13 4KGF 0 JRNL AUTH K.D.PIATKEVICH,V.N.MALASHKEVICH,K.S.MOROZOVA,N.A.NEMKOVICH, JRNL AUTH 2 S.C.ALMO,V.V.VERKHUSHA JRNL TITL EXTENDED STOKES SHIFT IN FLUORESCENT PROTEINS: JRNL TITL 2 CHROMOPHORE-PROTEIN INTERACTIONS IN A NEAR-INFRARED JRNL TITL 3 TAGRFP675 VARIANT. JRNL REF SCI REP V. 3 1847 2013 JRNL REFN ESSN 2045-2322 JRNL PMID 23677204 JRNL DOI 10.1038/SREP01847 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 32806 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1650 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2201 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.1890 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3556 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 192 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.30000 REMARK 3 B22 (A**2) : -0.30000 REMARK 3 B33 (A**2) : 0.61000 REMARK 3 B12 (A**2) : 0.00000 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): 0.046 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.122 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.491 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3705 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5008 ; 1.656 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 451 ; 7.557 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 170 ;36.297 ;24.176 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 651 ;17.138 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.985 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 518 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2831 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -10 A 9999 REMARK 3 ORIGIN FOR THE GROUP (A): -10.0449 34.9787 4.5048 REMARK 3 T TENSOR REMARK 3 T11: 0.0695 T22: 0.1926 REMARK 3 T33: 0.1419 T12: -0.0530 REMARK 3 T13: 0.0252 T23: -0.0956 REMARK 3 L TENSOR REMARK 3 L11: 1.1887 L22: 1.2309 REMARK 3 L33: 2.3518 L12: -0.1358 REMARK 3 L13: -0.6173 L23: -0.2194 REMARK 3 S TENSOR REMARK 3 S11: -0.0119 S12: 0.3097 S13: -0.1358 REMARK 3 S21: -0.0665 S22: -0.1510 S23: 0.0103 REMARK 3 S31: 0.3697 S32: -0.3503 S33: 0.1629 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B -10 B 9999 REMARK 3 ORIGIN FOR THE GROUP (A): -13.7936 37.1266 35.3898 REMARK 3 T TENSOR REMARK 3 T11: 0.0634 T22: 0.1207 REMARK 3 T33: 0.1286 T12: -0.0632 REMARK 3 T13: -0.0674 T23: 0.0910 REMARK 3 L TENSOR REMARK 3 L11: 1.6942 L22: 0.7421 REMARK 3 L33: 3.7703 L12: 0.2163 REMARK 3 L13: -1.7353 L23: -0.8430 REMARK 3 S TENSOR REMARK 3 S11: 0.0008 S12: -0.2886 S13: -0.1145 REMARK 3 S21: 0.1716 S22: -0.1787 S23: -0.0954 REMARK 3 S31: -0.1963 S32: 0.5661 S33: 0.1780 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: U VALUES : WITH TLS ADDED HYDROGENS REMARK 3 HAVE BEEN USED IF PRESENT IN THE INPUT REMARK 4 REMARK 4 4KGF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000079306. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35919 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 15.50 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.2 REMARK 200 DATA REDUNDANCY IN SHELL : 14.10 REMARK 200 R MERGE FOR SHELL (I) : 0.92100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4KGE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA-ACETATE, PH 4.5, 3.0M NACL. REMARK 280 THEN SOLUTION SLOWLY REPLACED WITH 0.1M TRIS-HCL, PH 8.0, 3.0M REMARK 280 NACL 8-10 MIN, COLOR CHANGE (DARKER), VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 72.66067 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 145.32133 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 108.99100 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 181.65167 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 36.33033 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 72.66067 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 145.32133 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 181.65167 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 108.99100 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 36.33033 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 300 REMARK: DIMERIC 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: 4110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 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 -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 GLY A -2 REMARK 465 ARG A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 LEU A 228 REMARK 465 GLY A 229 REMARK 465 HIS A 230 REMARK 465 LYS A 231 REMARK 465 LEU A 232 REMARK 465 ASN A 233 REMARK 465 MET B -11 REMARK 465 GLY B -10 REMARK 465 SER B -9 REMARK 465 HIS B -8 REMARK 465 HIS B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 GLY B -2 REMARK 465 ARG B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 PRO B 225 REMARK 465 SER B 226 REMARK 465 LYS B 227 REMARK 465 LEU B 228 REMARK 465 GLY B 229 REMARK 465 HIS B 230 REMARK 465 LYS B 231 REMARK 465 LEU B 232 REMARK 465 ASN B 233 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 PRO A 183 C - N - CA ANGL. DEV. = 11.0 DEGREES REMARK 500 ARG A 197 CA - C - O ANGL. DEV. = 12.8 DEGREES REMARK 500 ARG A 197 CA - C - O ANGL. DEV. = 12.9 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 A 20 -97.33 56.97 REMARK 500 PHE A 69 47.90 -97.80 REMARK 500 GLN A 74 -145.19 54.31 REMARK 500 ASN A 143 -169.25 -166.20 REMARK 500 ASP A 151 -142.61 76.28 REMARK 500 PRO A 183 -27.96 -28.78 REMARK 500 ALA A 184 -36.44 98.13 REMARK 500 PHE B 69 51.06 -98.54 REMARK 500 GLN B 74 -144.04 49.40 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 A 99 GLY A 100 -149.90 REMARK 500 GLY B 99 GLY B 100 -149.08 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 CL A 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KGE RELATED DB: PDB REMARK 900 PH 4.5 REMARK 900 RELATED ID: NYSGRC-031183 RELATED DB: TARGETTRACK DBREF 4KGF A -11 233 PDB 4KGF 4KGF -11 233 DBREF 4KGF B -11 233 PDB 4KGF 4KGF -11 233 SEQRES 1 A 243 MET GLY SER HIS HIS HIS HIS HIS HIS GLY ARG SER MET SEQRES 2 A 243 SER GLU LEU ILE LYS GLU ASN MET HIS MET LYS LEU TYR SEQRES 3 A 243 MET GLU GLY THR VAL ASN ASN HIS HIS PHE LYS CYS THR SEQRES 4 A 243 SER GLU GLY GLU GLY LYS PRO TYR GLU GLY THR GLN THR SEQRES 5 A 243 GLN ARG ILE LYS VAL VAL GLU GLY GLY PRO LEU PRO PHE SEQRES 6 A 243 ALA PHE ASP ILE LEU ALA THR SER PHE NRQ SER LYS THR SEQRES 7 A 243 PHE ILE ASN HIS THR GLN GLY ILE PRO ASP PHE TRP LYS SEQRES 8 A 243 GLN SER PHE PRO GLU GLY PHE THR TRP GLU ARG VAL THR SEQRES 9 A 243 THR TYR GLU ASP GLY GLY VAL LEU THR ALA THR GLN ASP SEQRES 10 A 243 THR SER LEU GLN ASP GLY CYS LEU ILE TYR ASN VAL LYS SEQRES 11 A 243 ILE ARG GLY VAL ASN PHE PRO SER ASN GLY PRO VAL MET SEQRES 12 A 243 GLN LYS LYS THR LEU GLY TRP GLU ALA ASN THR GLU MET SEQRES 13 A 243 MET TYR PRO ALA ASP GLY GLY LEU GLU GLY ARG ASN TYR SEQRES 14 A 243 MET ALA LEU LYS LEU VAL GLY GLY GLY HIS LEU ILE CYS SEQRES 15 A 243 SER LEU LYS THR THR TYR ARG SER LYS LYS PRO ALA LYS SEQRES 16 A 243 ASN LEU LYS MET PRO GLY VAL TYR TYR VAL ASP ARG ARG SEQRES 17 A 243 LEU GLU ARG ILE LYS GLU ALA ASP LYS GLU THR TYR VAL SEQRES 18 A 243 GLU GLN HIS GLU VAL ALA VAL ALA ARG TYR CYS ASP LEU SEQRES 19 A 243 PRO SER LYS LEU GLY HIS LYS LEU ASN SEQRES 1 B 243 MET GLY SER HIS HIS HIS HIS HIS HIS GLY ARG SER MET SEQRES 2 B 243 SER GLU LEU ILE LYS GLU ASN MET HIS MET LYS LEU TYR SEQRES 3 B 243 MET GLU GLY THR VAL ASN ASN HIS HIS PHE LYS CYS THR SEQRES 4 B 243 SER GLU GLY GLU GLY LYS PRO TYR GLU GLY THR GLN THR SEQRES 5 B 243 GLN ARG ILE LYS VAL VAL GLU GLY GLY PRO LEU PRO PHE SEQRES 6 B 243 ALA PHE ASP ILE LEU ALA THR SER PHE NRQ SER LYS THR SEQRES 7 B 243 PHE ILE ASN HIS THR GLN GLY ILE PRO ASP PHE TRP LYS SEQRES 8 B 243 GLN SER PHE PRO GLU GLY PHE THR TRP GLU ARG VAL THR SEQRES 9 B 243 THR TYR GLU ASP GLY GLY VAL LEU THR ALA THR GLN ASP SEQRES 10 B 243 THR SER LEU GLN ASP GLY CYS LEU ILE TYR ASN VAL LYS SEQRES 11 B 243 ILE ARG GLY VAL ASN PHE PRO SER ASN GLY PRO VAL MET SEQRES 12 B 243 GLN LYS LYS THR LEU GLY TRP GLU ALA ASN THR GLU MET SEQRES 13 B 243 MET TYR PRO ALA ASP GLY GLY LEU GLU GLY ARG ASN TYR SEQRES 14 B 243 MET ALA LEU LYS LEU VAL GLY GLY GLY HIS LEU ILE CYS SEQRES 15 B 243 SER LEU LYS THR THR TYR ARG SER LYS LYS PRO ALA LYS SEQRES 16 B 243 ASN LEU LYS MET PRO GLY VAL TYR TYR VAL ASP ARG ARG SEQRES 17 B 243 LEU GLU ARG ILE LYS GLU ALA ASP LYS GLU THR TYR VAL SEQRES 18 B 243 GLU GLN HIS GLU VAL ALA VAL ALA ARG TYR CYS ASP LEU SEQRES 19 B 243 PRO SER LYS LEU GLY HIS LYS LEU ASN MODRES 4KGF NRQ A 63 MET MODRES 4KGF NRQ A 63 TYR MODRES 4KGF NRQ A 63 GLY MODRES 4KGF NRQ B 63 MET MODRES 4KGF NRQ B 63 TYR MODRES 4KGF NRQ B 63 GLY HET NRQ A 63 23 HET NRQ B 63 36 HET CL A 500 1 HETNAM NRQ {(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO) HETNAM 2 NRQ PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1- HETNAM 3 NRQ YL}ACETIC ACID HETNAM CL CHLORIDE ION HETSYN NRQ CHROMOPHORE (MET-TYR-GLY) FORMUL 1 NRQ 2(C16 H17 N3 O4 S) FORMUL 3 CL CL 1- FORMUL 4 HOH *192(H2 O) HELIX 1 1 ALA A 54 PHE A 62 5 9 HELIX 2 2 SER A 66 ILE A 70 5 5 HELIX 3 3 TRP A 80 PHE A 84 5 5 HELIX 4 4 PRO B 34 GLU B 36 5 3 HELIX 5 5 ALA B 54 PHE B 62 5 9 HELIX 6 6 TRP B 80 PHE B 84 5 5 HELIX 7 7 GLY B 130 LYS B 135 1 6 HELIX 8 8 PRO B 183 LEU B 187 5 5 SHEET 1 A11 ASN A 71 HIS A 72 0 SHEET 2 A11 TYR A 210 ARG A 220 1 O ALA A 217 N ASN A 71 SHEET 3 A11 THR A 38 GLU A 47 -1 N ILE A 43 O VAL A 211 SHEET 4 A11 HIS A 22 GLY A 32 -1 N GLU A 29 O ARG A 42 SHEET 5 A11 MET A 9 VAL A 19 -1 N LEU A 13 O SER A 28 SHEET 6 A11 CYS A 114 VAL A 124 1 O GLY A 123 N THR A 18 SHEET 7 A11 VAL A 101 GLN A 111 -1 N SER A 109 O ILE A 116 SHEET 8 A11 PHE A 88 TYR A 96 -1 N PHE A 88 O THR A 108 SHEET 9 A11 HIS A 169 SER A 180 -1 O THR A 177 N GLU A 91 SHEET 10 A11 GLY A 153 LEU A 164 -1 N LEU A 154 O TYR A 178 SHEET 11 A11 THR A 137 TRP A 140 -1 N GLY A 139 O LYS A 163 SHEET 1 B 6 ASN A 71 HIS A 72 0 SHEET 2 B 6 TYR A 210 ARG A 220 1 O ALA A 217 N ASN A 71 SHEET 3 B 6 TYR A 193 ALA A 205 -1 N GLU A 200 O HIS A 214 SHEET 4 B 6 ASN A 143 ALA A 150 -1 N MET A 147 O TYR A 193 SHEET 5 B 6 GLY A 153 LEU A 164 -1 O GLU A 155 N TYR A 148 SHEET 6 B 6 THR A 137 TRP A 140 -1 N GLY A 139 O LYS A 163 SHEET 1 C11 ASN B 71 HIS B 72 0 SHEET 2 C11 TYR B 210 ARG B 220 1 O ALA B 217 N ASN B 71 SHEET 3 C11 THR B 38 GLU B 47 -1 N ILE B 43 O VAL B 211 SHEET 4 C11 HIS B 22 GLY B 32 -1 N GLU B 29 O ARG B 42 SHEET 5 C11 MET B 9 VAL B 19 -1 N MET B 11 O GLY B 30 SHEET 6 C11 CYS B 114 VAL B 124 1 O GLY B 123 N THR B 18 SHEET 7 C11 VAL B 101 GLN B 111 -1 N SER B 109 O ILE B 116 SHEET 8 C11 PHE B 88 TYR B 96 -1 N TRP B 90 O GLN B 106 SHEET 9 C11 HIS B 169 SER B 180 -1 O ARG B 179 N THR B 89 SHEET 10 C11 GLY B 153 LEU B 164 -1 N LEU B 154 O TYR B 178 SHEET 11 C11 THR B 137 TRP B 140 -1 N LEU B 138 O LYS B 163 SHEET 1 D 6 ASN B 71 HIS B 72 0 SHEET 2 D 6 TYR B 210 ARG B 220 1 O ALA B 217 N ASN B 71 SHEET 3 D 6 TYR B 193 ALA B 205 -1 N GLU B 200 O HIS B 214 SHEET 4 D 6 ASN B 143 ALA B 150 -1 N MET B 147 O TYR B 193 SHEET 5 D 6 GLY B 153 LEU B 164 -1 O ARG B 157 N MET B 146 SHEET 6 D 6 THR B 137 TRP B 140 -1 N LEU B 138 O LYS B 163 LINK C PHE A 62 N1 NRQ A 63 1555 1555 1.31 LINK C3 NRQ A 63 N SER A 66 1555 1555 1.33 LINK C PHE B 62 N1 NRQ B 63 1555 1555 1.31 LINK C3 NRQ B 63 N SER B 66 1555 1555 1.34 CISPEP 1 GLY A 49 PRO A 50 0 -7.09 CISPEP 2 PHE A 84 PRO A 85 0 12.72 CISPEP 3 GLY B 49 PRO B 50 0 -6.19 CISPEP 4 PHE B 84 PRO B 85 0 2.94 SITE 1 AC1 3 GLU A 145 ASN A 158 ARG A 197 CRYST1 105.893 105.893 217.982 90.00 90.00 120.00 P 61 2 2 24 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 0.009443 0.005452 0.000000 0.00000 SCALE2 0.000000 0.010904 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004588 0.00000