HEADER PROTEIN BINDING 16-JUN-17 5O99 TITLE UNCONVENTIONAL SH3 DOMAIN FROM THE POSTSYNAPTIC DENSITY SCAFFOLD TITLE 2 PROTEIN SHANK3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SH3 AND MULTIPLE ANKYRIN REPEAT DOMAINS PROTEIN 3; COMPND 3 CHAIN: B, A; COMPND 4 FRAGMENT: UNP RESIDUES 470-528; COMPND 5 SYNONYM: SHANK3,PROLINE-RICH SYNAPSE-ASSOCIATED PROTEIN 2,PROSAP2, COMPND 6 SPANK-2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: SHANK3, PROSAP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS POSTSYNAPTIC DENSITY, SCAFFOLDING PROTEIN, SH3 DOMAIN, NON-CANONICAL KEYWDS 2 BINDING SITE, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.K.PONNA,M.MYLLYKOSKI,T.M.BOECKERS,P.KURSULA REVDAT 3 08-MAY-24 5O99 1 REMARK REVDAT 2 02-AUG-17 5O99 1 REVDAT 1 05-JUL-17 5O99 0 JRNL AUTH S.K.PONNA,M.MYLLYKOSKI,T.M.BOECKERS,P.KURSULA JRNL TITL STRUCTURE OF AN UNCONVENTIONAL SH3 DOMAIN FROM THE JRNL TITL 2 POSTSYNAPTIC DENSITY PROTEIN SHANK3 AT ULTRAHIGH RESOLUTION. JRNL REF BIOCHEM. BIOPHYS. RES. V. 490 806 2017 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 28647360 JRNL DOI 10.1016/J.BBRC.2017.06.121 REMARK 2 REMARK 2 RESOLUTION. 0.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12RC1_2801: ???) 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.270 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.0 REMARK 3 NUMBER OF REFLECTIONS : 64681 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.112 REMARK 3 R VALUE (WORKING SET) : 0.097 REMARK 3 FREE R VALUE : 0.117 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1421 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 27.1808 - 1.8200 0.96 8556 175 0.0926 0.1307 REMARK 3 2 1.8200 - 1.4446 0.96 8460 173 0.1076 0.1234 REMARK 3 3 1.4446 - 1.2620 0.96 8409 171 0.1154 0.1299 REMARK 3 4 1.2620 - 1.1466 0.94 8216 168 0.1143 0.1274 REMARK 3 5 1.1466 - 1.0644 0.91 7912 162 0.1120 0.1253 REMARK 3 6 1.0644 - 1.0017 0.89 7880 160 0.1254 0.1337 REMARK 3 7 1.0017 - 0.9515 0.85 7401 151 0.1595 0.1549 REMARK 3 8 0.9515 - 0.9101 0.53 4661 96 0.2441 0.2597 REMARK 3 9 0.9101 - 0.8750 0.21 1862 38 0.4035 0.3390 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.20 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 : 0.019 988 REMARK 3 ANGLE : 1.472 1339 REMARK 3 CHIRALITY : 0.117 131 REMARK 3 PLANARITY : 0.009 176 REMARK 3 DIHEDRAL : 17.236 370 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 5O99 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200005402. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-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 : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 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 : 64681 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.870 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 (%) : 81.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 11.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.39500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTO-RICKSHAW REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS (PH 6.5), 32.5% REMARK 280 PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 26.45500 REMARK 290 SMTRY3 2 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: 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 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: 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 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 GLN B 528 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 B 623 O HOH B 637 1.73 REMARK 500 O8 BTB A 601 O HOH A 701 2.02 REMARK 500 O HOH B 603 O HOH B 641 2.19 REMARK 500 O HOH B 612 O HOH B 682 2.19 REMARK 500 O HOH B 686 O HOH B 690 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 VAL A 527 CB VAL A 527 CG1 -0.130 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 GLN B 484 36.70 -141.11 REMARK 500 GLN A 484 37.09 -142.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 725 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH B 726 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH B 727 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH B 728 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH B 729 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH B 730 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH B 731 DISTANCE = 7.27 ANGSTROMS REMARK 525 HOH B 732 DISTANCE = 7.96 ANGSTROMS REMARK 525 HOH B 733 DISTANCE = 8.01 ANGSTROMS REMARK 525 HOH B 734 DISTANCE = 8.09 ANGSTROMS REMARK 525 HOH A 790 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH A 791 DISTANCE = 7.05 ANGSTROMS REMARK 525 HOH A 792 DISTANCE = 7.21 ANGSTROMS REMARK 525 HOH A 793 DISTANCE = 7.39 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BTB A 601 DBREF 5O99 B 470 528 UNP Q9JLU4 SHAN3_RAT 470 528 DBREF 5O99 A 470 528 UNP Q9JLU4 SHAN3_RAT 470 528 SEQADV 5O99 SER B 469 UNP Q9JLU4 EXPRESSION TAG SEQADV 5O99 SER A 469 UNP Q9JLU4 EXPRESSION TAG SEQRES 1 B 60 SER VAL PRO GLY ARG LYS PHE ILE ALA VAL LYS ALA HIS SEQRES 2 B 60 SER PRO GLN GLY GLU GLY GLU ILE PRO LEU HIS ARG GLY SEQRES 3 B 60 GLU ALA VAL LYS VAL LEU SER ILE GLY GLU GLY GLY PHE SEQRES 4 B 60 TRP GLU GLY THR VAL LYS GLY ARG THR GLY TRP PHE PRO SEQRES 5 B 60 ALA ASP CYS VAL GLU GLU VAL GLN SEQRES 1 A 60 SER VAL PRO GLY ARG LYS PHE ILE ALA VAL LYS ALA HIS SEQRES 2 A 60 SER PRO GLN GLY GLU GLY GLU ILE PRO LEU HIS ARG GLY SEQRES 3 A 60 GLU ALA VAL LYS VAL LEU SER ILE GLY GLU GLY GLY PHE SEQRES 4 A 60 TRP GLU GLY THR VAL LYS GLY ARG THR GLY TRP PHE PRO SEQRES 5 A 60 ALA ASP CYS VAL GLU GLU VAL GLN HET BTB A 601 66 HETNAM BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL- HETNAM 2 BTB PROPANE-1,3-DIOL HETSYN BTB BIS-TRIS BUFFER FORMUL 3 BTB C8 H19 N O5 FORMUL 4 HOH *227(H2 O) SHEET 1 AA1 5 ARG B 515 PRO B 520 0 SHEET 2 AA1 5 PHE B 507 VAL B 512 -1 N TRP B 508 O PHE B 519 SHEET 3 AA1 5 ALA B 496 ILE B 502 -1 N SER B 501 O GLU B 509 SHEET 4 AA1 5 LYS B 474 ALA B 477 -1 N PHE B 475 O VAL B 497 SHEET 5 AA1 5 VAL B 524 GLU B 526 -1 O GLU B 525 N ILE B 476 SHEET 1 AA2 5 ARG A 515 PRO A 520 0 SHEET 2 AA2 5 PHE A 507 VAL A 512 -1 N TRP A 508 O PHE A 519 SHEET 3 AA2 5 ALA A 496 ILE A 502 -1 N LEU A 500 O GLU A 509 SHEET 4 AA2 5 LYS A 474 ALA A 477 -1 N PHE A 475 O VAL A 497 SHEET 5 AA2 5 VAL A 524 GLU A 526 -1 O GLU A 525 N ILE A 476 SITE 1 AC1 8 GLU A 486 GLU A 488 GLU A 504 TRP A 518 SITE 2 AC1 8 HOH A 701 HOH A 731 HOH A 742 LYS B 513 CRYST1 29.740 52.910 31.660 90.00 90.05 90.00 P 1 21 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 0.033625 0.000000 0.000030 0.00000 SCALE2 0.000000 0.018900 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031586 0.00000