HEADER SIGNALING PROTEIN 24-FEB-18 5ZDS TITLE CRYSTAL STRUCTURE OF THE SECOND PDZ DOMAIN OF FRMPD2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERM AND PDZ DOMAIN-CONTAINING 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 934-1027; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: FRMPD2, GM626; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FRMPD2, PDZ, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.LU,X.F.WANG REVDAT 3 03-APR-24 5ZDS 1 JRNL REVDAT 2 22-NOV-23 5ZDS 1 REMARK REVDAT 1 27-FEB-19 5ZDS 0 JRNL AUTH X.LU,Q.ZHANG,T.WANG JRNL TITL THE SECOND PDZ DOMAIN OF SCAFFOLD PROTEIN FRMPD2 BINDS TO JRNL TITL 2 GLUN2A OF NMDA RECEPTORS. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 516 63 2019 JRNL REFN ESSN 1090-2104 JRNL PMID 31196628 JRNL DOI 10.1016/J.BBRC.2019.05.087 REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 8610 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 860 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 32.2051 - 3.2700 0.99 1367 151 0.1803 0.2038 REMARK 3 2 3.2700 - 2.5959 1.00 1305 145 0.2002 0.2265 REMARK 3 3 2.5959 - 2.2678 1.00 1284 142 0.2085 0.2639 REMARK 3 4 2.2678 - 2.0605 1.00 1271 141 0.2016 0.2449 REMARK 3 5 2.0605 - 1.9128 1.00 1258 141 0.2065 0.2646 REMARK 3 6 1.9128 - 1.8000 1.00 1265 140 0.2254 0.2709 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.570 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 : 0.005 670 REMARK 3 ANGLE : 0.831 911 REMARK 3 CHIRALITY : 0.059 108 REMARK 3 PLANARITY : 0.006 119 REMARK 3 DIHEDRAL : 18.380 399 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -1.8541 11.8180 -9.8617 REMARK 3 T TENSOR REMARK 3 T11: 0.0271 T22: 0.0311 REMARK 3 T33: 0.0312 T12: -0.0007 REMARK 3 T13: 0.0117 T23: 0.0078 REMARK 3 L TENSOR REMARK 3 L11: 0.1176 L22: 0.3326 REMARK 3 L33: 0.2527 L12: -0.0635 REMARK 3 L13: -0.1042 L23: 0.1896 REMARK 3 S TENSOR REMARK 3 S11: -0.0293 S12: -0.0338 S13: -0.0330 REMARK 3 S21: 0.0003 S22: 0.0161 S23: 0.0547 REMARK 3 S31: -0.0111 S32: 0.0489 S33: -0.0557 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 5ZDS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1300006693. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-17 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97858 REMARK 200 MONOCHROMATOR : DCM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12699 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.5200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.700 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: 1VJ6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350 20%, SODIUM THIOCYANATE 0.2M, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 24.08800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.42100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.08800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.42100 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: 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 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 A1242 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1248 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 926 REMARK 465 SER A 927 REMARK 465 GLN A 928 REMARK 465 THR A 929 REMARK 465 ASN A 930 REMARK 465 THR A 931 REMARK 465 GLY A 932 REMARK 465 GLY A 1021 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 943 CG OD1 OD2 REMARK 470 GLN A1004 CG CD OE1 NE2 REMARK 470 ARG A1014 CG CD NE CZ NH1 NH2 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 1191 O HOH A 1227 2.14 REMARK 500 O HOH A 1233 O HOH A 1249 2.16 REMARK 500 OE2 GLU A 938 O HOH A 1101 2.19 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 LYS A 966 -65.38 -96.49 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 A1248 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A1249 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH A1250 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH A1251 DISTANCE = 7.72 ANGSTROMS REMARK 525 HOH A1252 DISTANCE = 7.75 ANGSTROMS DBREF1 5ZDS A 928 1021 UNP A0A140LI67_MOUSE DBREF2 5ZDS A A0A140LI67 934 1027 SEQADV 5ZDS GLY A 926 UNP A0A140LI6 EXPRESSION TAG SEQADV 5ZDS SER A 927 UNP A0A140LI6 EXPRESSION TAG SEQRES 1 A 96 GLY SER GLN THR ASN THR GLY GLU ILE TYR PHE VAL GLU SEQRES 2 A 96 LEU VAL LYS GLU ASP GLY THR LEU GLY PHE SER VAL THR SEQRES 3 A 96 GLY GLY ILE ASN THR SER VAL PRO HIS GLY GLY ILE TYR SEQRES 4 A 96 VAL LYS SER ILE ILE PRO GLY GLY PRO ALA ALA LYS GLU SEQRES 5 A 96 GLY GLN ILE LEU GLN GLY ASP ARG LEU LEU GLN VAL ASP SEQRES 6 A 96 GLY VAL SER LEU CYS GLY LEU THR HIS LYS GLN ALA VAL SEQRES 7 A 96 GLN CYS LEU LYS GLY PRO GLY GLN VAL ALA ARG LEU VAL SEQRES 8 A 96 LEU GLU ARG ARG GLY FORMUL 2 HOH *152(H2 O) HELIX 1 AA1 VAL A 958 GLY A 961 5 4 HELIX 2 AA2 GLY A 972 GLY A 978 1 7 HELIX 3 AA3 THR A 998 LYS A 1007 1 10 SHEET 1 AA1 4 ILE A 934 VAL A 940 0 SHEET 2 AA1 4 VAL A1012 GLU A1018 -1 O LEU A1015 N VAL A 937 SHEET 3 AA1 4 ARG A 985 VAL A 989 -1 N ARG A 985 O GLU A1018 SHEET 4 AA1 4 VAL A 992 SER A 993 -1 O VAL A 992 N VAL A 989 SHEET 1 AA2 2 PHE A 948 GLY A 952 0 SHEET 2 AA2 2 ILE A 963 ILE A 968 -1 O LYS A 966 N SER A 949 SSBOND 1 CYS A 995 CYS A 995 1555 2555 2.03 CRYST1 48.176 56.842 32.200 90.00 90.00 90.00 P 21 21 2 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 0.020757 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017593 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031056 0.00000