HEADER PROTEIN BINDING 04-MAR-14 4PQW TITLE CRYSTAL STRUCTURE OF PHOSPHOLIPASE C BETA 3 IN COMPLEX WITH PDZ1 OF TITLE 2 NHERF1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NA(+)/H(+) EXCHANGE REGULATORY COFACTOR NHE-RF1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 11-94; COMPND 5 SYNONYM: NHERF-1, EZRIN-RADIXIN-MOESIN-BINDING PHOSPHOPROTEIN 50, COMPND 6 EBP50, REGULATORY COFACTOR OF NA(+)/H(+) EXCHANGER, SODIUM-HYDROGEN COMPND 7 EXCHANGER REGULATORY FACTOR 1, SOLUTE CARRIER FAMILY 9 ISOFORM A3 COMPND 8 REGULATORY FACTOR 1; COMPND 9 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: NHERF, NHERF1, SLC9A3R1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSUMO KEYWDS NHERF1, PLCB3, SCAFFOLD PROTEIN, PANCREATIC CANCER, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.JIANG,S.WANG,J.HOLCOMB,L.TRESCOTT,X.GUAN,Y.HOU,J.BRUNZELLE, AUTHOR 2 N.SIRINUPONG,C.LI,Z.YANG REVDAT 3 20-SEP-23 4PQW 1 REMARK SEQADV LINK REVDAT 2 23-APR-14 4PQW 1 JRNL REVDAT 1 02-APR-14 4PQW 0 JRNL AUTH Y.JIANG,S.WANG,J.HOLCOMB,L.TRESCOTT,X.GUAN,Y.HOU, JRNL AUTH 2 J.BRUNZELLE,N.SIRINUPONG,C.LI,Z.YANG JRNL TITL CRYSTALLOGRAPHIC ANALYSIS OF NHERF1-PLC BETA 3 INTERACTION JRNL TITL 2 PROVIDES STRUCTURAL BASIS FOR CXCR2 SIGNALING IN PANCREATIC JRNL TITL 3 CANCER. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 446 638 2014 JRNL REFN ISSN 0006-291X JRNL PMID 24642259 JRNL DOI 10.1016/J.BBRC.2014.03.028 REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 17175 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 870 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 26.5493 - 2.6704 0.97 2801 124 0.1768 0.1687 REMARK 3 2 2.6704 - 2.1199 1.00 2747 158 0.1724 0.2013 REMARK 3 3 2.1199 - 1.8520 1.00 2731 135 0.1659 0.1888 REMARK 3 4 1.8520 - 1.6827 1.00 2677 159 0.1798 0.2381 REMARK 3 5 1.6827 - 1.5621 0.99 2701 147 0.2118 0.2808 REMARK 3 6 1.5621 - 1.4700 0.99 2648 147 0.2570 0.3108 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) : 24.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.80 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 : 0.005 712 REMARK 3 ANGLE : 0.954 963 REMARK 3 CHIRALITY : 0.050 108 REMARK 3 PLANARITY : 0.004 130 REMARK 3 DIHEDRAL : 13.865 277 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 4PQW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000085110. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1272 REMARK 200 MONOCHROMATOR : KOHZU REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17247 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 33.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.57500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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: PDB ENTRY 4JL7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE, PH 4.6, 2.5 M REMARK 280 SODIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.22667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.45333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.45333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.22667 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 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 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 332 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 343 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 373 LIES ON A SPECIAL POSITION. 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 379 O HOH A 382 1.84 REMARK 500 O HOH A 327 O HOH A 346 2.02 REMARK 500 O HOH A 336 O HOH A 357 2.07 REMARK 500 O HOH A 316 O HOH A 358 2.17 REMARK 500 O HOH A 377 O HOH A 381 2.18 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 ASN A 84 19.12 57.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 205 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 93 O REMARK 620 2 ASN A 96 O 75.5 REMARK 620 3 HOH A 330 O 137.0 104.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 205 DBREF 4PQW A 11 94 UNP O14745 NHRF1_HUMAN 11 94 SEQADV 4PQW GLY A 9 UNP O14745 EXPRESSION TAG SEQADV 4PQW MET A 10 UNP O14745 EXPRESSION TAG SEQADV 4PQW GLU A 95 UNP O14745 EXPRESSION TAG SEQADV 4PQW ASN A 96 UNP O14745 EXPRESSION TAG SEQADV 4PQW THR A 97 UNP O14745 EXPRESSION TAG SEQADV 4PQW GLN A 98 UNP O14745 EXPRESSION TAG SEQADV 4PQW LEU A 99 UNP O14745 EXPRESSION TAG SEQRES 1 A 91 GLY MET LEU PRO ARG LEU CYS CYS LEU GLU LYS GLY PRO SEQRES 2 A 91 ASN GLY TYR GLY PHE HIS LEU HIS GLY GLU LYS GLY LYS SEQRES 3 A 91 LEU GLY GLN TYR ILE ARG LEU VAL GLU PRO GLY SER PRO SEQRES 4 A 91 ALA GLU LYS ALA GLY LEU LEU ALA GLY ASP ARG LEU VAL SEQRES 5 A 91 GLU VAL ASN GLY GLU ASN VAL GLU LYS GLU THR HIS GLN SEQRES 6 A 91 GLN VAL VAL SER ARG ILE ARG ALA ALA LEU ASN ALA VAL SEQRES 7 A 91 ARG LEU LEU VAL VAL ASP PRO GLU GLU ASN THR GLN LEU HET CL A 201 1 HET CL A 202 1 HET CL A 203 1 HET CL A 204 1 HET NI A 205 1 HETNAM CL CHLORIDE ION HETNAM NI NICKEL (II) ION FORMUL 2 CL 4(CL 1-) FORMUL 6 NI NI 2+ FORMUL 7 HOH *93(H2 O) HELIX 1 1 SER A 46 ALA A 51 1 6 HELIX 2 2 THR A 71 ALA A 81 1 11 HELIX 3 3 ASP A 92 ASN A 96 5 5 SHEET 1 A 4 ARG A 13 GLU A 18 0 SHEET 2 A 4 ALA A 85 VAL A 91 -1 O LEU A 88 N CYS A 15 SHEET 3 A 4 ARG A 58 VAL A 62 -1 N VAL A 60 O LEU A 89 SHEET 4 A 4 GLU A 65 ASN A 66 -1 O GLU A 65 N VAL A 62 SHEET 1 B 2 HIS A 27 GLY A 30 0 SHEET 2 B 2 GLN A 37 ARG A 40 -1 O TYR A 38 N HIS A 29 LINK O PRO A 93 NI NI A 205 1555 1555 2.66 LINK O ASN A 96 NI NI A 205 1555 1555 2.61 LINK NI NI A 205 O HOH A 330 1555 1555 2.08 SITE 1 AC1 3 ARG A 40 LEU A 41 HOH A 307 SITE 1 AC2 5 ARG A 40 VAL A 91 ASP A 92 ASN A 96 SITE 2 AC2 5 HOH A 311 SITE 1 AC3 1 GLN A 98 SITE 1 AC4 4 ASN A 63 GLY A 64 ARG A 87 HOH A 308 SITE 1 AC5 4 PRO A 93 ASN A 96 THR A 97 HOH A 330 CRYST1 50.660 50.660 66.680 90.00 90.00 120.00 P 31 2 1 6 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 0.019739 0.011397 0.000000 0.00000 SCALE2 0.000000 0.022793 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014997 0.00000