HEADER SIGNALING PROTEIN 19-MAY-20 6X23 TITLE PDZ DOMAIN FROM CHOANOFLAGELLATE SHANK1 (MBSHANK1) BOUND TO GIRK3 TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MBSHANK1 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ DOMAIN (UNP RESIDUES 442-544); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: G PROTEIN-ACTIVATED INWARD RECTIFIER POTASSIUM CHANNEL 3; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: PEPTIDE (UNP RESIDUES 384-393); COMPND 10 SYNONYM: GIRK-3,INWARD RECTIFIER K(+) CHANNEL KIR3.3,POTASSIUM COMPND 11 CHANNEL,INWARDLY RECTIFYING SUBFAMILY J MEMBER 9; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MONOSIGA BREVICOLLIS; SOURCE 3 ORGANISM_COMMON: CHOANOFLAGELLATE; SOURCE 4 ORGANISM_TAXID: 81824; SOURCE 5 GENE: 28170; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A+; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS PDZ, PROTEIN-PROTEIN INTERACTION, PEPTIDE-BINDING DOMAIN, KEYWDS 2 CHOANOFLAGELLATE, MONOSIGA BREVICOLLIS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.GAO,I.G.P.MACKLEY,J.F.AMACHER REVDAT 2 06-MAR-24 6X23 1 REMARK REVDAT 1 25-NOV-20 6X23 0 JRNL AUTH M.GAO,I.G.P.MACKLEY,S.MESBAHI-VASEY,H.A.BAMONTE, JRNL AUTH 2 S.A.STRUYVENBERG,L.LANDOLT,N.J.PEDERSON,L.I.WILLIAMS, JRNL AUTH 3 C.D.BAHL,L.BROOKS 3RD,J.F.AMACHER JRNL TITL STRUCTURAL CHARACTERIZATION AND COMPUTATIONAL ANALYSIS OF JRNL TITL 2 PDZ DOMAINS IN MONOSIGA BREVICOLLIS. JRNL REF PROTEIN SCI. V. 29 2226 2020 JRNL REFN ESSN 1469-896X JRNL PMID 32914530 JRNL DOI 10.1002/PRO.3947 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 64.1 REMARK 3 NUMBER OF REFLECTIONS : 3941 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 189 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 36.1600 - 2.1540 0.64 3752 189 0.2060 0.2534 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.04 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 : 0.010 753 REMARK 3 ANGLE : 1.344 1008 REMARK 3 CHIRALITY : 0.061 106 REMARK 3 PLANARITY : 0.007 134 REMARK 3 DIHEDRAL : 17.747 454 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 6X23 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1000249440. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977410 REMARK 200 MONOCHROMATOR : SI(220) 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 : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6160 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 36.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.57 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.16000 REMARK 200 FOR THE DATA SET : 12.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 12.68 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.55000 REMARK 200 FOR SHELL : 2.030 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 (%): 42.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.25 M SODIUM CHLORIDE, 0.1 M BIS REMARK 280 -TRIS, PH 5.5, 32% W/V PEG3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 16.53500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.43000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.34500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.43000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.53500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.34500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A 440 REMARK 465 PRO A 441 REMARK 465 GLN A 442 REMARK 465 ARG A 443 REMARK 465 ASN A 444 REMARK 465 GLY A 445 REMARK 465 ARG A 446 REMARK 465 SER A 473 REMARK 465 ALA A 474 REMARK 465 ALA A 475 REMARK 465 GLU A 476 REMARK 465 GLN A 477 REMARK 465 THR A 478 REMARK 465 GLY A 542 REMARK 465 PRO A 543 REMARK 465 ASP A 544 REMARK 465 LEU B 1 REMARK 465 PRO B 2 REMARK 465 PRO B 3 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 606 O HOH A 615 2.10 REMARK 500 OG1 THR A 471 OG SER B 6 2.16 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 A 480 -60.97 -150.28 REMARK 500 SER B 6 111.59 175.37 REMARK 500 REMARK 500 REMARK: NULL DBREF 6X23 A 442 544 UNP A9V7E4 A9V7E4_MONBE 442 544 DBREF 6X23 B 1 10 UNP Q92806 KCNJ9_HUMAN 384 393 SEQADV 6X23 GLY A 440 UNP A9V7E4 EXPRESSION TAG SEQADV 6X23 PRO A 441 UNP A9V7E4 EXPRESSION TAG SEQRES 1 A 105 GLY PRO GLN ARG ASN GLY ARG ALA PRO GLU GLY LYS MET SEQRES 2 A 105 ASP LEU ILE ILE MET ARG GLY ASP LYS GLY PHE GLY PHE SEQRES 3 A 105 ARG LEU SER GLY ALA THR HIS SER ALA ALA GLU GLN THR SEQRES 4 A 105 ALA GLN GLY GLN TRP VAL ARG ASN VAL ASP PRO ASP GLY SEQRES 5 A 105 GLN ALA ALA ARG ALA GLY LEU GLN ALA GLY ASP ARG LEU SEQRES 6 A 105 LEU GLU LEU ASN GLY VAL ASP VAL SER PHE TRP SER HIS SEQRES 7 A 105 ARG LYS VAL VAL ASP GLU ILE LYS ARG SER GLY ASP VAL SEQRES 8 A 105 VAL ALA PHE ARG ILE ALA ARG ARG LEU SER PRO GLY PRO SEQRES 9 A 105 ASP SEQRES 1 B 10 LEU PRO PRO PRO GLU SER GLU SER LYS VAL FORMUL 3 HOH *23(H2 O) HELIX 1 AA1 GLY A 491 GLY A 497 1 7 HELIX 2 AA2 SER A 516 SER A 527 1 12 SHEET 1 AA1 4 GLU A 449 MET A 457 0 SHEET 2 AA1 4 VAL A 530 ARG A 538 -1 O PHE A 533 N LEU A 454 SHEET 3 AA1 4 ARG A 503 LEU A 507 -1 N LEU A 505 O ARG A 534 SHEET 4 AA1 4 VAL A 510 ASP A 511 -1 O VAL A 510 N LEU A 507 SHEET 1 AA2 3 TRP A 483 VAL A 487 0 SHEET 2 AA2 3 PHE A 465 SER A 468 -1 N SER A 468 O TRP A 483 SHEET 3 AA2 3 GLU B 7 LYS B 9 -1 O SER B 8 N LEU A 467 CRYST1 33.070 40.690 78.860 90.00 90.00 90.00 P 21 21 21 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 0.030239 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024576 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012681 0.00000