HEADER STRUCTURAL PROTEIN 10-MAY-10 3MYL TITLE INSIGHTS INTO THE IMPORTANCE OF HYDROGEN BONDING IN THE GAMMA- TITLE 2 PHOSPHATE BINDING POCKET OF MYOSIN: STRUCTURAL AND FUNCTIONAL STUDIES TITLE 3 OF SER236 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOSIN-2 HEAVY CHAIN; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: MYOSIN II HEAVY CHAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICTYOSTELIUM DISCOIDEUM; SOURCE 3 ORGANISM_COMMON: SLIME MOLD; SOURCE 4 ORGANISM_TAXID: 44689; SOURCE 5 GENE: DDB_G0286355, MHCA; SOURCE 6 EXPRESSION_SYSTEM: DICTYOSTELIUM DISCOIDEUM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 44689; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ORF+; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDXA KEYWDS S1DC, MYOSIN, S236A, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.J.FRYE,V.A.KLENCHIN,C.R.BAGSHAW,I.RAYMENT REVDAT 3 06-SEP-23 3MYL 1 REMARK SEQADV LINK REVDAT 2 23-JUN-10 3MYL 1 JRNL REVDAT 1 26-MAY-10 3MYL 0 JRNL AUTH J.J.FRYE,V.A.KLENCHIN,C.R.BAGSHAW,I.RAYMENT JRNL TITL INSIGHTS INTO THE IMPORTANCE OF HYDROGEN BONDING IN THE JRNL TITL 2 GAMMA-PHOSPHATE BINDING POCKET OF MYOSIN: STRUCTURAL AND JRNL TITL 3 FUNCTIONAL STUDIES OF SERINE 236 JRNL REF BIOCHEMISTRY V. 49 4897 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20459085 JRNL DOI 10.1021/BI1001344 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 65472 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3483 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4682 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.1970 REMARK 3 BIN FREE R VALUE SET COUNT : 244 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5917 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 736 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.40000 REMARK 3 B22 (A**2) : 0.34000 REMARK 3 B33 (A**2) : -0.74000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.096 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.323 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6099 ; 0.026 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8253 ; 1.958 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 755 ; 6.772 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 309 ;35.369 ;24.822 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1076 ;16.437 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;17.446 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 908 ; 0.160 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4662 ; 0.011 ; 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): 3729 ; 1.271 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6020 ; 2.152 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2370 ; 3.403 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2226 ; 5.084 ; 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 : MASK 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3MYL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-10. REMARK 100 THE DEPOSITION ID IS D_1000059156. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-08 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 : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00707 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69055 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : 0.11500 REMARK 200 FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.40600 REMARK 200 R SYM FOR SHELL (I) : 0.40600 REMARK 200 FOR SHELL : 3.900 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: PDB ENTRY 1VOM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5% MEPEG5K, 117MM AMMONIUM ACETATE, REMARK 280 100MM HEPPS, 2MM MGCL2, 2MM SODIUM PYROPHOSPHATE , PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 52.02250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 90.38950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 52.02250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 90.38950 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 X 1 REMARK 465 ASN X 203 REMARK 465 GLN X 204 REMARK 465 ALA X 205 REMARK 465 ASN X 206 REMARK 465 GLY X 207 REMARK 465 SER X 208 REMARK 465 PHE X 503 REMARK 465 ILE X 504 REMARK 465 ASP X 505 REMARK 465 PHE X 506 REMARK 465 ALA X 620A REMARK 465 GLY X 624 REMARK 465 ALA X 625 REMARK 465 ASN X 626 REMARK 465 LEU X 760 REMARK 465 PRO X 761 REMARK 465 ASN X 762 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP X 23 CG OD1 OD2 REMARK 470 LYS X 26 NZ REMARK 470 LYS X 63 CE NZ REMARK 470 LYS X 73 CE NZ REMARK 470 ARG X 131 CZ NH1 NH2 REMARK 470 ARG X 202 CD NE CZ NH1 NH2 REMARK 470 ARG X 232 CZ NH1 NH2 REMARK 470 GLU X 291 CD OE1 OE2 REMARK 470 LYS X 294 CG CD CE NZ REMARK 470 LYS X 316 CG CD CE NZ REMARK 470 GLU X 339 CD OE1 OE2 REMARK 470 MET X 342 CE REMARK 470 GLU X 444 CG CD OE1 OE2 REMARK 470 ARG X 445 CG CD NE CZ NH1 NH2 REMARK 470 LYS X 462 CD CE NZ REMARK 470 LYS X 496 NZ REMARK 470 LEU X 508 CG CD1 CD2 REMARK 470 LYS X 553 NZ REMARK 470 LYS X 622 CG CD CE NZ REMARK 470 LYS X 670 CG CD CE NZ REMARK 470 LYS X 703 CE NZ REMARK 470 LYS X 728 CE NZ REMARK 470 ARG X 758 CG CD NE CZ NH1 NH2 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 OD1 ASP X 45 NH2 ARG X 677 1.53 REMARK 500 O HOH X 1100 O HOH X 1771 1.63 REMARK 500 O HOH X 1555 O HOH X 1767 1.87 REMARK 500 O HOH X 1116 O HOH X 1540 2.03 REMARK 500 OE1 GLU X 492 O HOH X 1633 2.05 REMARK 500 O HOH X 1725 O HOH X 1726 2.10 REMARK 500 O HOH X 1257 O HOH X 1540 2.10 REMARK 500 O HOH X 1367 O HOH X 1487 2.11 REMARK 500 O HOH X 1293 O HOH X 1780 2.13 REMARK 500 O ALA X 363 N GLU X 365 2.14 REMARK 500 O HOH X 1328 O HOH X 1719 2.17 REMARK 500 CB GLN X 443 O HOH X 1724 2.18 REMARK 500 O HOH X 1353 O HOH X 1582 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 TYR X 473 CD1 TYR X 473 CE1 0.092 REMARK 500 GLU X 636 CB GLU X 636 CG 0.132 REMARK 500 GLU X 636 CG GLU X 636 CD 0.158 REMARK 500 GLU X 636 CD GLU X 636 OE1 0.072 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 X 107 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG X 238 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG X 238 NE - CZ - NH2 ANGL. DEV. = -6.3 DEGREES REMARK 500 LEU X 431 CA - CB - CG ANGL. DEV. = 18.7 DEGREES REMARK 500 ARG X 677 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG X 689 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG X 689 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 PRO X 713 C - N - CD ANGL. DEV. = -20.9 DEGREES REMARK 500 ARG X 738 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG X 747 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG X 753 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG X 753 NE - CZ - NH2 ANGL. DEV. = -5.0 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 THR X 56 -168.87 -115.50 REMARK 500 THR X 274 -6.79 70.08 REMARK 500 ALA X 299 -152.24 -122.33 REMARK 500 ALA X 363 -167.35 134.18 REMARK 500 GLU X 365 84.84 66.55 REMARK 500 ALA X 367 121.12 74.43 REMARK 500 ARG X 445 65.53 -117.62 REMARK 500 SER X 465 -163.67 -126.22 REMARK 500 ASP X 509 -45.41 -26.01 REMARK 500 LYS X 553 13.19 59.21 REMARK 500 PRO X 713 86.22 43.89 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 VAL X 712 PRO X 713 74.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG X 998 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR X 186 OG1 REMARK 620 2 SER X 237 OG 87.5 REMARK 620 3 POP X 999 O4 175.3 88.8 REMARK 620 4 POP X 999 O1 91.3 173.9 92.7 REMARK 620 5 HOH X1111 O 82.4 91.6 94.8 94.2 REMARK 620 6 HOH X1129 O 91.9 82.3 90.5 91.8 171.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 998 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP X 999 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MYH RELATED DB: PDB REMARK 900 RELATED ID: 3MYK RELATED DB: PDB DBREF 3MYL X 2 759 UNP P08799 MYS2_DICDI 2 759 SEQADV 3MYL GLY X 1 UNP P08799 EXPRESSION TAG SEQADV 3MYL ALA X 236 UNP P08799 SER 236 ENGINEERED MUTATION SEQADV 3MYL LEU X 760 UNP P08799 EXPRESSION TAG SEQADV 3MYL PRO X 761 UNP P08799 EXPRESSION TAG SEQADV 3MYL ASN X 762 UNP P08799 EXPRESSION TAG SEQRES 1 X 762 GLY ASN PRO ILE HIS ASP ARG THR SER ASP TYR HIS LYS SEQRES 2 X 762 TYR LEU LYS VAL LYS GLN GLY ASP SER ASP LEU PHE LYS SEQRES 3 X 762 LEU THR VAL SER ASP LYS ARG TYR ILE TRP TYR ASN PRO SEQRES 4 X 762 ASP PRO LYS GLU ARG ASP SER TYR GLU CYS GLY GLU ILE SEQRES 5 X 762 VAL SER GLU THR SER ASP SER PHE THR PHE LYS THR VAL SEQRES 6 X 762 ASP GLY GLN ASP ARG GLN VAL LYS LYS ASP ASP ALA ASN SEQRES 7 X 762 GLN ARG ASN PRO ILE LYS PHE ASP GLY VAL GLU ASP MET SEQRES 8 X 762 SER GLU LEU SER TYR LEU ASN GLU PRO ALA VAL PHE HIS SEQRES 9 X 762 ASN LEU ARG VAL ARG TYR ASN GLN ASP LEU ILE TYR THR SEQRES 10 X 762 TYR SER GLY LEU PHE LEU VAL ALA VAL ASN PRO PHE LYS SEQRES 11 X 762 ARG ILE PRO ILE TYR THR GLN GLU MET VAL ASP ILE PHE SEQRES 12 X 762 LYS GLY ARG ARG ARG ASN GLU VAL ALA PRO HIS ILE PHE SEQRES 13 X 762 ALA ILE SER ASP VAL ALA TYR ARG SER MET LEU ASP ASP SEQRES 14 X 762 ARG GLN ASN GLN SER LEU LEU ILE THR GLY GLU SER GLY SEQRES 15 X 762 ALA GLY LYS THR GLU ASN THR LYS LYS VAL ILE GLN TYR SEQRES 16 X 762 LEU ALA SER VAL ALA GLY ARG ASN GLN ALA ASN GLY SER SEQRES 17 X 762 GLY VAL LEU GLU GLN GLN ILE LEU GLN ALA ASN PRO ILE SEQRES 18 X 762 LEU GLU ALA PHE GLY ASN ALA LYS THR THR ARG ASN ASN SEQRES 19 X 762 ASN ALA SER ARG PHE GLY LYS PHE ILE GLU ILE GLN PHE SEQRES 20 X 762 ASN SER ALA GLY PHE ILE SER GLY ALA SER ILE GLN SER SEQRES 21 X 762 TYR LEU LEU GLU LYS SER ARG VAL VAL PHE GLN SER GLU SEQRES 22 X 762 THR GLU ARG ASN TYR HIS ILE PHE TYR GLN LEU LEU ALA SEQRES 23 X 762 GLY ALA THR ALA GLU GLU LYS LYS ALA LEU HIS LEU ALA SEQRES 24 X 762 GLY PRO GLU SER PHE ASN TYR LEU ASN GLN SER GLY CYS SEQRES 25 X 762 VAL ASP ILE LYS GLY VAL SER ASP SER GLU GLU PHE LYS SEQRES 26 X 762 ILE THR ARG GLN ALA MET ASP ILE VAL GLY PHE SER GLN SEQRES 27 X 762 GLU GLU GLN MET SER ILE PHE LYS ILE ILE ALA GLY ILE SEQRES 28 X 762 LEU HIS LEU GLY ASN ILE LYS PHE GLU LYS GLY ALA GLY SEQRES 29 X 762 GLU GLY ALA VAL LEU LYS ASP LYS THR ALA LEU ASN ALA SEQRES 30 X 762 ALA SER THR VAL PHE GLY VAL ASN PRO SER VAL LEU GLU SEQRES 31 X 762 LYS ALA LEU MET GLU PRO ARG ILE LEU ALA GLY ARG ASP SEQRES 32 X 762 LEU VAL ALA GLN HIS LEU ASN VAL GLU LYS SER SER SER SEQRES 33 X 762 SER ARG ASP ALA LEU VAL LYS ALA LEU TYR GLY ARG LEU SEQRES 34 X 762 PHE LEU TRP LEU VAL LYS LYS ILE ASN ASN VAL LEU CYS SEQRES 35 X 762 GLN GLU ARG LYS ALA TYR PHE ILE GLY VAL LEU ASP ILE SEQRES 36 X 762 SER GLY PHE GLU ILE PHE LYS VAL ASN SER PHE GLU GLN SEQRES 37 X 762 LEU CYS ILE ASN TYR THR ASN GLU LYS LEU GLN GLN PHE SEQRES 38 X 762 PHE ASN HIS HIS MET PHE LYS LEU GLU GLN GLU GLU TYR SEQRES 39 X 762 LEU LYS GLU LYS ILE ASN TRP THR PHE ILE ASP PHE GLY SEQRES 40 X 762 LEU ASP SER GLN ALA THR ILE ASP LEU ILE ASP GLY ARG SEQRES 41 X 762 GLN PRO PRO GLY ILE LEU ALA LEU LEU ASP GLU GLN SER SEQRES 42 X 762 VAL PHE PRO ASN ALA THR ASP ASN THR LEU ILE THR LYS SEQRES 43 X 762 LEU HIS SER HIS PHE SER LYS LYS ASN ALA LYS TYR GLU SEQRES 44 X 762 GLU PRO ARG PHE SER LYS THR GLU PHE GLY VAL THR HIS SEQRES 45 X 762 TYR ALA GLY GLN VAL MET TYR GLU ILE GLN ASP TRP LEU SEQRES 46 X 762 GLU LYS ASN LYS ASP PRO LEU GLN GLN ASP LEU GLU LEU SEQRES 47 X 762 CYS PHE LYS ASP SER SER ASP ASN VAL VAL THR LYS LEU SEQRES 48 X 762 PHE ASN ASP PRO ASN ILE ALA SER ARG ALA LYS LYS GLY SEQRES 49 X 762 ALA ASN PHE ILE THR VAL ALA ALA GLN TYR LYS GLU GLN SEQRES 50 X 762 LEU ALA SER LEU MET ALA THR LEU GLU THR THR ASN PRO SEQRES 51 X 762 HIS PHE VAL ARG CYS ILE ILE PRO ASN ASN LYS GLN LEU SEQRES 52 X 762 PRO ALA LYS LEU GLU ASP LYS VAL VAL LEU ASP GLN LEU SEQRES 53 X 762 ARG CYS ASN GLY VAL LEU GLU GLY ILE ARG ILE THR ARG SEQRES 54 X 762 LYS GLY PHE PRO ASN ARG ILE ILE TYR ALA ASP PHE VAL SEQRES 55 X 762 LYS ARG TYR TYR LEU LEU ALA PRO ASN VAL PRO ARG ASP SEQRES 56 X 762 ALA GLU ASP SER GLN LYS ALA THR ASP ALA VAL LEU LYS SEQRES 57 X 762 HIS LEU ASN ILE ASP PRO GLU GLN TYR ARG PHE GLY ILE SEQRES 58 X 762 THR LYS ILE PHE PHE ARG ALA GLY GLN LEU ALA ARG ILE SEQRES 59 X 762 GLU GLU ALA ARG GLU LEU PRO ASN HET MG X 998 1 HET POP X 999 9 HETNAM MG MAGNESIUM ION HETNAM POP PYROPHOSPHATE 2- FORMUL 2 MG MG 2+ FORMUL 3 POP H2 O7 P2 2- FORMUL 4 HOH *736(H2 O) HELIX 1 1 SER X 9 LYS X 16 1 8 HELIX 2 2 LEU X 24 VAL X 29 5 6 HELIX 3 3 ASP X 75 ALA X 77 5 3 HELIX 4 4 PRO X 82 ASP X 86 5 5 HELIX 5 5 ASP X 90 LEU X 94 5 5 HELIX 6 6 ASN X 98 GLN X 112 1 15 HELIX 7 7 THR X 136 LYS X 144 1 9 HELIX 8 8 ARG X 147 VAL X 151 5 5 HELIX 9 9 HIS X 154 ARG X 170 1 17 HELIX 10 10 GLY X 184 GLY X 201 1 18 HELIX 11 11 GLY X 209 GLY X 226 1 18 HELIX 12 12 GLU X 264 VAL X 269 5 6 HELIX 13 13 TYR X 278 ALA X 288 1 11 HELIX 14 14 THR X 289 LEU X 296 1 8 HELIX 15 15 GLY X 300 PHE X 304 5 5 HELIX 16 16 SER X 319 GLY X 335 1 17 HELIX 17 17 SER X 337 ILE X 357 1 21 HELIX 18 18 LYS X 372 GLY X 383 1 12 HELIX 19 19 ASN X 385 GLU X 395 1 11 HELIX 20 20 ASN X 410 CYS X 442 1 33 HELIX 21 21 SER X 465 LYS X 498 1 34 HELIX 22 22 SER X 510 GLY X 519 1 10 HELIX 23 23 GLY X 524 SER X 533 1 10 HELIX 24 24 THR X 539 SER X 552 1 14 HELIX 25 25 ASP X 583 ASP X 590 1 8 HELIX 26 26 GLN X 593 ASP X 602 1 10 HELIX 27 27 VAL X 607 ASP X 614 1 8 HELIX 28 28 ASP X 614 SER X 619 1 6 HELIX 29 29 THR X 629 THR X 647 1 19 HELIX 30 30 GLU X 668 ASN X 679 1 12 HELIX 31 31 GLY X 680 LYS X 690 1 11 HELIX 32 32 TYR X 698 TYR X 706 1 9 HELIX 33 33 LEU X 707 ALA X 709 5 3 HELIX 34 34 ASP X 718 LEU X 730 1 13 HELIX 35 35 ASP X 733 GLU X 735 5 3 HELIX 36 36 GLY X 749 GLU X 756 1 8 SHEET 1 A 5 ASP X 69 LYS X 73 0 SHEET 2 A 5 SER X 59 LYS X 63 -1 N PHE X 60 O VAL X 72 SHEET 3 A 5 GLU X 48 GLU X 55 -1 N SER X 54 O THR X 61 SHEET 4 A 5 TYR X 34 TYR X 37 -1 N ILE X 35 O GLY X 50 SHEET 5 A 5 ASN X 78 GLN X 79 -1 O ASN X 78 N TRP X 36 SHEET 1 B 7 TYR X 116 SER X 119 0 SHEET 2 B 7 PHE X 122 VAL X 126 -1 O VAL X 124 N THR X 117 SHEET 3 B 7 ASN X 649 ILE X 656 1 O ARG X 654 N LEU X 123 SHEET 4 B 7 GLN X 173 THR X 178 1 N LEU X 176 O VAL X 653 SHEET 5 B 7 TYR X 448 ASP X 454 1 O LEU X 453 N ILE X 177 SHEET 6 B 7 GLY X 240 PHE X 247 -1 N ILE X 243 O VAL X 452 SHEET 7 B 7 ILE X 253 TYR X 261 -1 O TYR X 261 N GLY X 240 SHEET 1 C 2 ASN X 227 ALA X 228 0 SHEET 2 C 2 ALA X 236 SER X 237 -1 O ALA X 236 N ALA X 228 SHEET 1 D 2 ARG X 397 ALA X 400 0 SHEET 2 D 2 ASP X 403 ALA X 406 -1 O VAL X 405 N ILE X 398 SHEET 1 E 3 TYR X 558 GLU X 559 0 SHEET 2 E 3 GLU X 567 HIS X 572 -1 O GLY X 569 N GLU X 559 SHEET 3 E 3 GLY X 575 GLU X 580 -1 O TYR X 579 N PHE X 568 SHEET 1 F 3 ASN X 694 ILE X 697 0 SHEET 2 F 3 LYS X 743 PHE X 746 -1 O PHE X 746 N ASN X 694 SHEET 3 F 3 TYR X 737 PHE X 739 -1 N ARG X 738 O PHE X 745 LINK OG1 THR X 186 MG MG X 998 1555 1555 2.06 LINK OG SER X 237 MG MG X 998 1555 1555 2.12 LINK MG MG X 998 O4 POP X 999 1555 1555 2.05 LINK MG MG X 998 O1 POP X 999 1555 1555 2.12 LINK MG MG X 998 O HOH X1111 1555 1555 2.19 LINK MG MG X 998 O HOH X1129 1555 1555 2.05 CISPEP 1 GLU X 365 GLY X 366 0 15.58 CISPEP 2 GLN X 521 PRO X 522 0 0.00 SITE 1 AC1 5 THR X 186 SER X 237 POP X 999 HOH X1111 SITE 2 AC1 5 HOH X1129 SITE 1 AC2 16 GLU X 180 SER X 181 GLY X 182 ALA X 183 SITE 2 AC2 16 GLY X 184 LYS X 185 THR X 186 ASN X 233 SITE 3 AC2 16 ALA X 236 SER X 237 MG X 998 HOH X1118 SITE 4 AC2 16 HOH X1129 HOH X1262 HOH X1301 HOH X1781 CRYST1 104.045 180.779 53.890 90.00 90.00 90.00 P 21 21 2 4 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 0.009611 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005532 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018556 0.00000