HEADER METAL BINDING PROTEIN 03-SEP-13 4MJJ TITLE CRYSTAL STRUCTURE OF THE C2A DOMAIN OF DOC2A COMPND MOL_ID: 1; COMPND 2 MOLECULE: DOUBLE C2-LIKE DOMAIN-CONTAINING PROTEIN ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C2A, UNP RESIDUES 81-217; COMPND 5 SYNONYM: DOC2, DOC2-ALPHA; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DOC2A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS C2 DOMAIN, DOC2A, CALCIUM BINDING PROTEIN, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Q.Q.HUANG REVDAT 1 30-OCT-13 4MJJ 0 JRNL AUTH Q.Q.HUANG JRNL TITL CRYSTAL STRUCTURE OF THE C2A DOMAIN OF DOC2A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 9644 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 960 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 21.2165 - 3.8199 0.97 1287 143 0.2102 0.2622 REMARK 3 2 3.8199 - 3.0348 1.00 1292 143 0.2091 0.2455 REMARK 3 3 3.0348 - 2.6520 0.98 1245 136 0.2319 0.2729 REMARK 3 4 2.6520 - 2.4099 0.97 1244 137 0.2172 0.2627 REMARK 3 5 2.4099 - 2.2374 0.96 1232 131 0.2341 0.2761 REMARK 3 6 2.2374 - 2.1056 0.96 1220 138 0.2343 0.3306 REMARK 3 7 2.1056 - 2.0002 0.92 1164 132 0.2362 0.2866 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 948 REMARK 3 ANGLE : 1.172 1276 REMARK 3 CHIRALITY : 0.083 148 REMARK 3 PLANARITY : 0.004 161 REMARK 3 DIHEDRAL : 15.718 365 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4MJJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-13. REMARK 100 THE RCSB ID CODE IS RCSB081989. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-13 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 : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15658 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.27500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG400, 100MM TRIS-HCL, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 41.98850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.53200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.98850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.53200 REMARK 290 SMTRY3 4 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 BIOMT1 2 -1.000000 0.000000 0.000000 36.15310 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -52.50487 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 388 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 301 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 346 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 350 LIES ON A SPECIAL POSITION. 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 80 REMARK 465 SER A 81 REMARK 465 TYR A 82 REMARK 465 ASP A 83 REMARK 465 SER A 84 REMARK 465 ASP A 85 REMARK 465 ASP A 86 REMARK 465 ALA A 87 REMARK 465 THR A 88 REMARK 465 MET A 119 REMARK 465 ASP A 120 REMARK 465 PHE A 121 REMARK 465 ASN A 122 REMARK 465 GLY A 123 REMARK 465 LEU A 124 REMARK 465 ALA A 125 REMARK 465 LYS A 184 REMARK 465 LEU A 185 REMARK 465 SER A 186 REMARK 465 HIS A 187 REMARK 465 ASN A 188 REMARK 465 VAL A 217 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 O HOH A 383 O HOH A 384 1.86 REMARK 500 O HOH A 365 O HOH A 371 1.93 REMARK 500 O HOH A 311 O HOH A 353 1.94 REMARK 500 O HOH A 354 O HOH A 376 1.95 REMARK 500 O HOH A 359 O HOH A 361 2.02 REMARK 500 O HOH A 370 O HOH A 382 2.04 REMARK 500 OE2 GLU A 158 O HOH A 347 2.08 REMARK 500 O HOH A 367 O HOH A 370 2.12 REMARK 500 N ASP A 126 O HOH A 376 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 353 O HOH A 354 3555 2.17 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 LEU A 111 -68.73 -91.85 REMARK 500 REMARK 500 REMARK: NULL DBREF 4MJJ A 81 217 UNP Q14183 DOC2A_HUMAN 81 217 SEQADV 4MJJ GLY A 80 UNP Q14183 EXPRESSION TAG SEQRES 1 A 138 GLY SER TYR ASP SER ASP ASP ALA THR ALA LEU GLY THR SEQRES 2 A 138 LEU GLU PHE ASP LEU LEU TYR ASP ARG ALA SER CYS THR SEQRES 3 A 138 LEU HIS CYS SER ILE LEU ARG ALA LYS GLY LEU LYS PRO SEQRES 4 A 138 MET ASP PHE ASN GLY LEU ALA ASP PRO TYR VAL LYS LEU SEQRES 5 A 138 HIS LEU LEU PRO GLY ALA CYS LYS ALA ASN LYS LEU LYS SEQRES 6 A 138 THR LYS THR GLN ARG ASN THR LEU ASN PRO VAL TRP ASN SEQRES 7 A 138 GLU ASP LEU THR TYR SER GLY ILE THR ASP ASP ASP ILE SEQRES 8 A 138 THR HIS LYS VAL LEU ARG ILE ALA VAL CYS ASP GLU ASP SEQRES 9 A 138 LYS LEU SER HIS ASN GLU PHE ILE GLY GLU ILE ARG VAL SEQRES 10 A 138 PRO LEU ARG ARG LEU LYS PRO SER GLN LYS LYS HIS PHE SEQRES 11 A 138 ASN ILE CYS LEU GLU ARG GLN VAL FORMUL 2 HOH *89(H2 O) HELIX 1 1 CYS A 138 ALA A 140 5 3 HELIX 2 2 THR A 166 LYS A 173 1 8 HELIX 3 3 ARG A 199 LEU A 201 5 3 SHEET 1 A 4 VAL A 155 TYR A 162 0 SHEET 2 A 4 THR A 105 LYS A 114 -1 N ILE A 110 O GLU A 158 SHEET 3 A 4 THR A 92 ASP A 100 -1 N LEU A 98 O HIS A 107 SHEET 4 A 4 LYS A 207 CYS A 212 -1 O PHE A 209 N PHE A 95 SHEET 1 B 4 LYS A 142 LYS A 144 0 SHEET 2 B 4 PRO A 127 LEU A 134 -1 N LEU A 131 O LEU A 143 SHEET 3 B 4 VAL A 174 ASP A 181 -1 O VAL A 174 N LEU A 134 SHEET 4 B 4 PHE A 190 PRO A 197 -1 O GLY A 192 N VAL A 179 SSBOND 1 CYS A 104 CYS A 138 1555 2554 2.04 CISPEP 1 LEU A 134 PRO A 135 0 10.23 CRYST1 83.977 33.064 63.748 90.00 124.55 90.00 C 1 2 1 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 0.011908 0.000000 0.008200 0.00000 SCALE2 0.000000 0.030244 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019046 0.00000