PDB Short entry for 5H4Z HEADER METAL BINDING PROTEIN 02-NOV-16 5H4Z TITLE CRYSTAL STRUCTURE OF S202G MUTANT OF HUMAN SYT-5 C2A DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTOTAGMIN-5; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 102-242; COMPND 5 SYNONYM: SYNAPTOTAGMIN V,SYTV; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SYT5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P28 KEYWDS METAL BINDING PROTEIN, MUTANT EXPDTA X-RAY DIFFRACTION AUTHOR X.QIU,J.GE,X.YAN,Y.GAO,M.TENG,L.NIU REVDAT 3 16-AUG-17 5H4Z 1 REMARK REVDAT 2 11-JAN-17 5H4Z 1 JRNL REVDAT 1 30-NOV-16 5H4Z 0 JRNL AUTH X.QIU,J.GE,Y.GAO,M.TENG,L.NIU JRNL TITL STRUCTURAL ANALYSIS OF CA(2+)-BINDING POCKET OF JRNL TITL 2 SYNAPTOTAGMIN 5 C2A DOMAIN JRNL REF INT. J. BIOL. MACROMOL. V. 95 946 2017 JRNL REFN ISSN 1879-0003 JRNL PMID 27793683 JRNL DOI 10.1016/J.IJBIOMAC.2016.10.083 REMARK 2 REMARK 2 RESOLUTION. 3.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 9496 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 474 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) : 3.01 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.09 REMARK 3 REFLECTION IN BIN (WORKING SET) : 570 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 36 REMARK 3 BIN FREE R VALUE : 0.4720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1992 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 47 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.62000 REMARK 3 B22 (A**2) : 3.78000 REMARK 3 B33 (A**2) : -2.16000 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): 0.772 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.368 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.248 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.452 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.916 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.869 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2044 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1375 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2774 ; 1.331 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3343 ; 0.834 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 257 ; 7.007 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 92 ;35.763 ;23.913 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 324 ;20.259 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;20.763 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 301 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2301 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 424 ; 0.001 ; 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): 1275 ; 0.673 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 523 ; 0.058 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2041 ; 1.264 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 769 ; 1.126 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 732 ; 2.044 ; 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS, SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/ REMARK 3 F_PLUS COLUMNS. REMARK 4 REMARK 4 5H4Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1300002031. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97916 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9990 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 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 : 6.400 REMARK 200 R MERGE (I) : 0.16700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.83700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 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: 5H4Y REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CALCIUM ACETATE, 0.1M SODIUM REMARK 280 ACETATE PH 4.0, 10%(W/V) PEG4000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 54.73200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.73200 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 38.00250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 59.32800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.00250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 59.32800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 54.73200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.00250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 59.32800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 54.73200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.00250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 59.32800 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 TOTAL BURIED SURFACE AREA: 150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 93 REMARK 465 GLY A 94 REMARK 465 HIS A 95 REMARK 465 HIS A 96 REMARK 465 HIS A 97 REMARK 465 HIS A 98 REMARK 465 HIS A 99 REMARK 465 HIS A 100 REMARK 465 MET A 101 REMARK 465 GLN A 102 REMARK 465 VAL A 103 REMARK 465 ALA A 104 REMARK 465 ARG A 234 REMARK 465 GLU A 235 REMARK 465 GLU A 236 REMARK 465 GLN A 237 REMARK 465 GLU A 238 REMARK 465 LYS A 239 REMARK 465 LEU A 240 REMARK 465 GLY A 241 REMARK 465 ASP A 242 REMARK 465 MET B 93 REMARK 465 GLY B 94 REMARK 465 HIS B 95 REMARK 465 HIS B 96 REMARK 465 HIS B 97 REMARK 465 HIS B 98 REMARK 465 HIS B 99 REMARK 465 HIS B 100 REMARK 465 MET B 101 REMARK 465 GLN B 102 REMARK 465 VAL B 103 REMARK 465 ALA B 104 REMARK 465 ASP B 105 REMARK 465 ARG B 234 REMARK 465 GLU B 235 REMARK 465 GLU B 236 REMARK 465 GLN B 237 REMARK 465 GLU B 238 REMARK 465 LYS B 239 REMARK 465 LEU B 240 REMARK 465 GLY B 241 REMARK 465 ASP B 242 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 A 105 OD1 OD2 REMARK 470 LYS A 106 CD CE NZ REMARK 470 GLN A 121 OE1 NE2 REMARK 470 ARG A 149 CZ NH1 NH2 REMARK 470 ARG A 157 NE CZ NH1 NH2 REMARK 470 ARG A 159 CD NE CZ NH1 NH2 REMARK 470 ARG A 166 CD NE CZ NH1 NH2 REMARK 470 LYS A 180 NZ REMARK 470 ARG A 203 CD NE CZ NH1 NH2 REMARK 470 ARG A 221 CZ NH1 NH2 REMARK 470 LYS B 106 CB CG CD CE NZ REMARK 470 GLN B 121 OE1 NE2 REMARK 470 ARG B 149 NH1 NH2 REMARK 470 LYS B 156 CD CE NZ REMARK 470 ARG B 157 NE CZ NH1 NH2 REMARK 470 ARG B 159 NH1 NH2 REMARK 470 LYS B 163 NZ REMARK 470 ARG B 166 CD NE CZ NH1 NH2 REMARK 470 GLU B 185 OE1 OE2 REMARK 470 ARG B 221 CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE2 GLN A 111 OE2 GLU B 108 8555 2.09 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 PRO A 233 C - N - CD ANGL. DEV. = -13.2 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 ASP A 145 69.91 -117.90 REMARK 500 GLN A 167 75.69 51.76 REMARK 500 TYR A 183 -37.07 -37.18 REMARK 500 PHE A 201 62.40 -116.61 REMARK 500 GLU B 108 113.37 11.02 REMARK 500 LEU B 130 -67.08 -92.00 REMARK 500 SER B 143 -159.95 -125.93 REMARK 500 ASP B 155 99.53 -63.47 REMARK 500 ARG B 158 70.43 -68.77 REMARK 500 GLN B 167 77.95 25.97 REMARK 500 PHE B 201 -60.16 -99.86 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 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 138 O REMARK 620 2 ASP A 139 OD1 87.9 REMARK 620 3 ASP A 197 OD2 91.0 81.8 REMARK 620 4 ASP A 199 OD1 164.7 78.5 80.3 REMARK 620 5 ASP A 199 OD2 142.2 129.5 98.8 52.4 REMARK 620 6 ASP A 205 OD2 83.2 165.6 87.1 108.7 61.2 REMARK 620 7 ASP A 218 OD1 78.4 106.9 28.7 98.8 93.0 60.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 139 OD1 REMARK 620 2 ASP A 139 OD2 49.3 REMARK 620 3 ASP A 145 OD2 119.5 71.3 REMARK 620 4 ASP A 197 OD1 94.9 84.9 90.3 REMARK 620 5 ASP A 197 OD2 63.7 89.3 134.4 46.0 REMARK 620 6 PHE A 198 O 163.2 147.4 76.7 89.1 109.1 REMARK 620 7 ASP A 199 OD1 72.3 121.5 160.0 105.4 64.4 90.9 REMARK 620 8 HOH A 404 O 76.4 75.0 78.0 159.1 137.3 104.7 90.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 199 OD2 REMARK 620 2 ARG A 203 O 83.2 REMARK 620 3 ASP A 205 OD1 77.6 82.2 REMARK 620 4 HOH A 417 O 89.3 88.6 164.8 REMARK 620 5 HOH A 416 O 163.8 95.7 86.2 106.8 REMARK 620 6 ASP A 218 OD2 66.9 66.0 19.1 146.3 97.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU B 138 O REMARK 620 2 ASP B 139 OD1 84.5 REMARK 620 3 ASP B 197 OD2 81.1 77.0 REMARK 620 4 ASP B 199 OD1 147.4 70.3 73.6 REMARK 620 5 ASP B 199 OD2 155.8 118.2 95.2 49.3 REMARK 620 6 ASP B 205 OD2 85.4 155.2 79.0 109.0 70.4 REMARK 620 7 HOH B 405 O 101.8 131.3 151.5 110.3 70.5 73.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 139 OD1 REMARK 620 2 ASP B 139 OD2 55.2 REMARK 620 3 ASP B 145 OD2 129.4 74.2 REMARK 620 4 ASP B 197 OD1 88.6 89.8 92.8 REMARK 620 5 ASP B 197 OD2 60.7 98.2 136.3 43.6 REMARK 620 6 PHE B 198 O 147.5 156.2 82.9 85.0 94.1 REMARK 620 7 ASP B 199 OD1 77.6 130.3 148.6 105.1 67.1 73.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 199 OD2 REMARK 620 2 ARG B 203 O 93.7 REMARK 620 3 ASP B 205 OD1 92.6 74.4 REMARK 620 4 ASP B 205 OD2 56.0 99.2 43.1 REMARK 620 5 HOH B 405 O 73.9 159.7 89.8 60.5 REMARK 620 6 HOH B 403 O 148.5 62.4 62.5 105.1 121.6 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 CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5H4Y RELATED DB: PDB DBREF 5H4Z A 102 242 UNP O00445 SYT5_HUMAN 102 242 DBREF 5H4Z B 102 242 UNP O00445 SYT5_HUMAN 102 242 SEQADV 5H4Z MET A 93 UNP O00445 INITIATING METHIONINE SEQADV 5H4Z GLY A 94 UNP O00445 EXPRESSION TAG SEQADV 5H4Z HIS A 95 UNP O00445 EXPRESSION TAG SEQADV 5H4Z HIS A 96 UNP O00445 EXPRESSION TAG SEQADV 5H4Z HIS A 97 UNP O00445 EXPRESSION TAG SEQADV 5H4Z HIS A 98 UNP O00445 EXPRESSION TAG SEQADV 5H4Z HIS A 99 UNP O00445 EXPRESSION TAG SEQADV 5H4Z HIS A 100 UNP O00445 EXPRESSION TAG SEQADV 5H4Z MET A 101 UNP O00445 EXPRESSION TAG SEQADV 5H4Z GLN A 111 UNP O00445 ARG 111 ENGINEERED MUTATION SEQADV 5H4Z GLY A 202 UNP O00445 SER 202 ENGINEERED MUTATION SEQADV 5H4Z MET B 93 UNP O00445 INITIATING METHIONINE SEQADV 5H4Z GLY B 94 UNP O00445 EXPRESSION TAG SEQADV 5H4Z HIS B 95 UNP O00445 EXPRESSION TAG SEQADV 5H4Z HIS B 96 UNP O00445 EXPRESSION TAG SEQADV 5H4Z HIS B 97 UNP O00445 EXPRESSION TAG SEQADV 5H4Z HIS B 98 UNP O00445 EXPRESSION TAG SEQADV 5H4Z HIS B 99 UNP O00445 EXPRESSION TAG SEQADV 5H4Z HIS B 100 UNP O00445 EXPRESSION TAG SEQADV 5H4Z MET B 101 UNP O00445 EXPRESSION TAG SEQADV 5H4Z GLN B 111 UNP O00445 ARG 111 ENGINEERED MUTATION SEQADV 5H4Z GLY B 202 UNP O00445 SER 202 ENGINEERED MUTATION SEQRES 1 A 150 MET GLY HIS HIS HIS HIS HIS HIS MET GLN VAL ALA ASP SEQRES 2 A 150 LYS HIS GLU LEU GLY GLN LEU GLN TYR SER LEU ASP TYR SEQRES 3 A 150 ASP PHE GLN SER GLY GLN LEU LEU VAL GLY ILE LEU GLN SEQRES 4 A 150 ALA MET GLY LEU ALA ALA LEU ASP LEU GLY GLY SER SER SEQRES 5 A 150 ASP PRO TYR VAL ARG VAL TYR LEU LEU PRO ASP LYS ARG SEQRES 6 A 150 ARG ARG TYR GLU THR LYS VAL HIS ARG GLN THR LEU ASN SEQRES 7 A 150 PRO HIS PHE GLY GLU THR PHE ALA PHE LYS VAL PRO TYR SEQRES 8 A 150 VAL GLU LEU GLY GLY ARG VAL LEU VAL MET ALA VAL TYR SEQRES 9 A 150 ASP PHE ASP ARG PHE GLY ARG ASN ASP ALA ILE GLY GLU SEQRES 10 A 150 VAL ARG VAL PRO MET SER SER VAL ASP LEU GLY ARG PRO SEQRES 11 A 150 VAL GLN ALA TRP ARG GLU LEU GLN ALA ALA PRO ARG GLU SEQRES 12 A 150 GLU GLN GLU LYS LEU GLY ASP SEQRES 1 B 150 MET GLY HIS HIS HIS HIS HIS HIS MET GLN VAL ALA ASP SEQRES 2 B 150 LYS HIS GLU LEU GLY GLN LEU GLN TYR SER LEU ASP TYR SEQRES 3 B 150 ASP PHE GLN SER GLY GLN LEU LEU VAL GLY ILE LEU GLN SEQRES 4 B 150 ALA MET GLY LEU ALA ALA LEU ASP LEU GLY GLY SER SER SEQRES 5 B 150 ASP PRO TYR VAL ARG VAL TYR LEU LEU PRO ASP LYS ARG SEQRES 6 B 150 ARG ARG TYR GLU THR LYS VAL HIS ARG GLN THR LEU ASN SEQRES 7 B 150 PRO HIS PHE GLY GLU THR PHE ALA PHE LYS VAL PRO TYR SEQRES 8 B 150 VAL GLU LEU GLY GLY ARG VAL LEU VAL MET ALA VAL TYR SEQRES 9 B 150 ASP PHE ASP ARG PHE GLY ARG ASN ASP ALA ILE GLY GLU SEQRES 10 B 150 VAL ARG VAL PRO MET SER SER VAL ASP LEU GLY ARG PRO SEQRES 11 B 150 VAL GLN ALA TRP ARG GLU LEU GLN ALA ALA PRO ARG GLU SEQRES 12 B 150 GLU GLN GLU LYS LEU GLY ASP HET CA A 301 1 HET CA A 302 1 HET CA A 303 1 HET CA B 301 1 HET CA B 302 1 HET CA B 303 1 HET CL B 304 1 HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION FORMUL 3 CA 6(CA 2+) FORMUL 9 CL CL 1- FORMUL 10 HOH *47(H2 O) HELIX 1 AA1 SER A 215 VAL A 217 5 3 HELIX 2 AA2 TYR B 183 GLY B 187 5 5 HELIX 3 AA3 SER B 215 VAL B 217 5 3 SHEET 1 AA1 4 HIS A 172 LYS A 180 0 SHEET 2 AA1 4 GLN A 124 MET A 133 -1 N ILE A 129 O GLU A 175 SHEET 3 AA1 4 GLN A 111 ASP A 119 -1 N GLN A 111 O MET A 133 SHEET 4 AA1 4 VAL A 223 GLU A 228 -1 O ARG A 227 N LEU A 112 SHEET 1 AA2 4 ASP A 155 GLU A 161 0 SHEET 2 AA2 4 PRO A 146 LEU A 153 -1 N VAL A 150 O TYR A 160 SHEET 3 AA2 4 VAL A 190 ASP A 197 -1 O ALA A 194 N ARG A 149 SHEET 4 AA2 4 ASP A 205 PRO A 213 -1 O VAL A 212 N LEU A 191 SHEET 1 AA3 4 HIS B 172 LYS B 180 0 SHEET 2 AA3 4 GLN B 124 MET B 133 -1 N VAL B 127 O PHE B 177 SHEET 3 AA3 4 GLN B 111 ASP B 119 -1 N ASP B 117 O LEU B 126 SHEET 4 AA3 4 VAL B 223 GLU B 228 -1 O ARG B 227 N LEU B 112 SHEET 1 AA4 4 ASP B 155 GLU B 161 0 SHEET 2 AA4 4 PRO B 146 LEU B 153 -1 N VAL B 150 O TYR B 160 SHEET 3 AA4 4 VAL B 190 ASP B 197 -1 O TYR B 196 N TYR B 147 SHEET 4 AA4 4 ASP B 205 PRO B 213 -1 O ASP B 205 N ASP B 197 LINK O LEU A 138 CA CA A 302 1555 1555 2.42 LINK OD1 ASP A 139 CA CA A 301 1555 1555 2.58 LINK OD1 ASP A 139 CA CA A 302 1555 1555 2.32 LINK OD2 ASP A 139 CA CA A 301 1555 1555 2.71 LINK OD2 ASP A 145 CA CA A 301 1555 1555 2.19 LINK OD1 ASP A 197 CA CA A 301 1555 1555 2.32 LINK OD2 ASP A 197 CA CA A 301 1555 1555 3.03 LINK OD2 ASP A 197 CA CA A 302 1555 1555 2.24 LINK O PHE A 198 CA CA A 301 1555 1555 2.50 LINK OD1 ASP A 199 CA CA A 301 1555 1555 2.37 LINK OD1 ASP A 199 CA CA A 302 1555 1555 2.31 LINK OD2 ASP A 199 CA CA A 302 1555 1555 2.63 LINK OD2 ASP A 199 CA CA A 303 1555 1555 2.30 LINK O ARG A 203 CA CA A 303 1555 1555 2.42 LINK OD1 ASP A 205 CA CA A 303 1555 1555 2.36 LINK OD2 ASP A 205 CA CA A 302 1555 1555 2.35 LINK O LEU B 138 CA CA B 302 1555 1555 2.24 LINK OD1 ASP B 139 CA CA B 301 1555 1555 2.44 LINK OD1 ASP B 139 CA CA B 302 1555 1555 2.30 LINK OD2 ASP B 139 CA CA B 301 1555 1555 2.30 LINK OD2 ASP B 145 CA CA B 301 1555 1555 2.25 LINK OD1 ASP B 197 CA CA B 301 1555 1555 2.54 LINK OD2 ASP B 197 CA CA B 301 1555 1555 3.16 LINK OD2 ASP B 197 CA CA B 302 1555 1555 2.35 LINK O PHE B 198 CA CA B 301 1555 1555 2.33 LINK OD1 ASP B 199 CA CA B 301 1555 1555 2.26 LINK OD1 ASP B 199 CA CA B 302 1555 1555 2.77 LINK OD2 ASP B 199 CA CA B 302 1555 1555 2.43 LINK OD2 ASP B 199 CA CA B 303 1555 1555 2.34 LINK O ARG B 203 CA CA B 303 1555 1555 2.61 LINK OD1 ASP B 205 CA CA B 303 1555 1555 2.77 LINK OD2 ASP B 205 CA CA B 302 1555 1555 2.17 LINK OD2 ASP B 205 CA CA B 303 1555 1555 3.13 LINK CA CA A 301 O HOH A 404 1555 1555 2.37 LINK CA CA A 303 O HOH A 417 1555 1555 2.59 LINK CA CA A 303 O HOH A 416 1555 1555 2.32 LINK CA CA B 302 O HOH B 405 1555 1555 2.68 LINK CA CA B 303 O HOH B 405 1555 1555 2.57 LINK CA CA B 303 O HOH B 403 1555 1555 2.67 LINK OD1 ASP A 218 CA CA A 302 1555 8555 2.22 LINK OD2 ASP A 218 CA CA A 303 1555 8555 2.04 CISPEP 1 LEU A 153 PRO A 154 0 6.53 CISPEP 2 LEU B 153 PRO B 154 0 4.80 SITE 1 AC1 7 ASP A 139 ASP A 145 ASP A 197 PHE A 198 SITE 2 AC1 7 ASP A 199 CA A 302 HOH A 404 SITE 1 AC2 7 LEU A 138 ASP A 139 ASP A 197 ASP A 199 SITE 2 AC2 7 ASP A 205 ASP A 218 CA A 301 SITE 1 AC3 6 ASP A 199 ARG A 203 ASP A 205 ASP A 218 SITE 2 AC3 6 HOH A 416 HOH A 417 SITE 1 AC4 5 ASP B 139 ASP B 145 ASP B 197 PHE B 198 SITE 2 AC4 5 ASP B 199 SITE 1 AC5 6 LEU B 138 ASP B 139 ASP B 197 ASP B 199 SITE 2 AC5 6 ASP B 205 HOH B 405 SITE 1 AC6 5 ASP B 199 ARG B 203 ASP B 205 HOH B 403 SITE 2 AC6 5 HOH B 405 SITE 1 AC7 2 GLU A 228 GLU B 228 CRYST1 76.005 118.656 109.464 90.00 90.00 90.00 C 2 2 21 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 0.013157 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008428 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009135 0.00000