HEADER PROTEIN BINDING 28-AUG-17 5OVA TITLE APO PDZ DOMAIN FROM RAT SHANK3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SH3 AND MULTIPLE ANKYRIN REPEAT DOMAINS PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SHANK3,PROLINE-RICH SYNAPSE-ASSOCIATED PROTEIN 2,PROSAP2, COMPND 5 SPANK-2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: SHANK3, PROSAP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PDZ DOMAIN, PEPTIDE BINDING, POST-SYNAPTIC DENSITY, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.K.PONNA,M.MYLLYKOSKI,T.M.BOECKERS,P.KURSULA REVDAT 2 11-JUL-18 5OVA 1 JRNL REVDAT 1 07-MAR-18 5OVA 0 JRNL AUTH S.K.PONNA,S.RUSKAMO,M.MYLLYKOSKI,C.KELLER,T.M.BOECKERS, JRNL AUTH 2 P.KURSULA JRNL TITL STRUCTURAL BASIS FOR PDZ DOMAIN INTERACTIONS IN THE JRNL TITL 2 POST-SYNAPTIC DENSITY SCAFFOLDING PROTEIN SHANK3. JRNL REF J. NEUROCHEM. V. 145 449 2018 JRNL REFN ESSN 1471-4159 JRNL PMID 29473168 JRNL DOI 10.1111/JNC.14322 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 7984 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.281 REMARK 3 R VALUE (WORKING SET) : 0.279 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.840 REMARK 3 FREE R VALUE TEST SET COUNT : 786 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 25.2732 - 4.1743 0.99 1284 139 0.2185 0.2289 REMARK 3 2 4.1743 - 3.3156 0.99 1211 129 0.2677 0.2710 REMARK 3 3 3.3156 - 2.8972 1.00 1201 134 0.3603 0.3683 REMARK 3 4 2.8972 - 2.6326 0.98 1165 125 0.3680 0.4741 REMARK 3 5 2.6326 - 2.4441 0.99 1169 130 0.3872 0.4414 REMARK 3 6 2.4441 - 2.3001 0.98 1168 129 0.4152 0.4756 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 41.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 59.30 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 : 0.004 1427 REMARK 3 ANGLE : 0.707 1929 REMARK 3 CHIRALITY : 0.051 225 REMARK 3 PLANARITY : 0.006 247 REMARK 3 DIHEDRAL : 22.421 839 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 5OVA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1200006423. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 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 PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8035 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, 2.0 M AMMONIUM REMARK 280 SULPHATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.54000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.25000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.26500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.25000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.54000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.26500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 LYS A 599 REMARK 465 ALA A 600 REMARK 465 GLU A 601 REMARK 465 THR A 602 REMARK 465 ALA B 598 REMARK 465 LYS B 599 REMARK 465 ALA B 600 REMARK 465 GLU B 601 REMARK 465 THR B 602 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 ILE A 604 58.55 -98.35 REMARK 500 ILE B 604 56.73 -103.76 REMARK 500 GLU B 605 -2.61 -144.55 REMARK 500 VAL B 650 -92.48 -101.77 REMARK 500 REMARK 500 REMARK: NULL DBREF 5OVA A 580 674 UNP Q9JLU4 SHAN3_RAT 570 664 DBREF 5OVA B 580 674 UNP Q9JLU4 SHAN3_RAT 570 664 SEQADV 5OVA SER A 579 UNP Q9JLU4 EXPRESSION TAG SEQADV 5OVA SER B 579 UNP Q9JLU4 EXPRESSION TAG SEQRES 1 A 96 SER VAL ALA ILE LEU GLN LYS ARG ASP HIS GLU GLY PHE SEQRES 2 A 96 GLY PHE VAL LEU ARG GLY ALA LYS ALA GLU THR PRO ILE SEQRES 3 A 96 GLU GLU PHE THR PRO THR PRO ALA PHE PRO ALA LEU GLN SEQRES 4 A 96 TYR LEU GLU SER VAL ASP VAL GLU GLY VAL ALA TRP LYS SEQRES 5 A 96 ALA GLY LEU ARG THR GLY ASP PHE LEU ILE GLU VAL ASN SEQRES 6 A 96 GLY VAL ASN VAL VAL LYS VAL GLY HIS LYS GLN VAL VAL SEQRES 7 A 96 GLY LEU ILE ARG GLN GLY GLY ASN ARG LEU VAL MET LYS SEQRES 8 A 96 VAL VAL SER VAL THR SEQRES 1 B 96 SER VAL ALA ILE LEU GLN LYS ARG ASP HIS GLU GLY PHE SEQRES 2 B 96 GLY PHE VAL LEU ARG GLY ALA LYS ALA GLU THR PRO ILE SEQRES 3 B 96 GLU GLU PHE THR PRO THR PRO ALA PHE PRO ALA LEU GLN SEQRES 4 B 96 TYR LEU GLU SER VAL ASP VAL GLU GLY VAL ALA TRP LYS SEQRES 5 B 96 ALA GLY LEU ARG THR GLY ASP PHE LEU ILE GLU VAL ASN SEQRES 6 B 96 GLY VAL ASN VAL VAL LYS VAL GLY HIS LYS GLN VAL VAL SEQRES 7 B 96 GLY LEU ILE ARG GLN GLY GLY ASN ARG LEU VAL MET LYS SEQRES 8 B 96 VAL VAL SER VAL THR FORMUL 3 HOH *6(H2 O) HELIX 1 AA1 GLY A 626 ALA A 631 1 6 HELIX 2 AA2 GLY A 651 GLY A 662 1 12 HELIX 3 AA3 GLY B 626 ALA B 631 1 6 HELIX 4 AA4 GLY B 651 GLY B 662 1 12 SHEET 1 AA1 4 VAL A 580 GLN A 584 0 SHEET 2 AA1 4 ARG A 665 SER A 672 -1 O LEU A 666 N LEU A 583 SHEET 3 AA1 4 ASP A 637 VAL A 642 -1 N ILE A 640 O LYS A 669 SHEET 4 AA1 4 VAL A 645 ASN A 646 -1 O VAL A 645 N VAL A 642 SHEET 1 AA2 2 PHE A 593 GLY A 597 0 SHEET 2 AA2 2 GLN A 617 VAL A 622 -1 O GLU A 620 N VAL A 594 SHEET 1 AA3 4 VAL B 580 GLN B 584 0 SHEET 2 AA3 4 ARG B 665 SER B 672 -1 O LEU B 666 N LEU B 583 SHEET 3 AA3 4 ASP B 637 VAL B 642 -1 N ILE B 640 O LYS B 669 SHEET 4 AA3 4 VAL B 645 ASN B 646 -1 O VAL B 645 N VAL B 642 SHEET 1 AA4 2 PHE B 593 ARG B 596 0 SHEET 2 AA4 2 TYR B 618 VAL B 622 -1 O GLU B 620 N VAL B 594 CRYST1 45.080 48.530 78.500 90.00 90.00 90.00 P 21 21 21 8 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 0.022183 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020606 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012739 0.00000