PDB Short entry for 1G9O HEADER SIGNALING PROTEIN 26-NOV-00 1G9O TITLE FIRST PDZ DOMAIN OF THE HUMAN NA+/H+ EXCHANGER REGULATORY FACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: NHE-RF; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ1 DOMAIN; COMPND 5 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; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); 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: PGEX-2T KEYWDS PDZ DOMAIN, NHERF, COMPLEX, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.KARTHIKEYAN,T.LEUNG,G.BIRRANE,G.WEBSTER,J.A.A.LADIAS REVDAT 4 07-FEB-24 1G9O 1 SEQADV REVDAT 3 24-FEB-09 1G9O 1 VERSN REVDAT 2 01-APR-03 1G9O 1 JRNL REVDAT 1 23-MAY-01 1G9O 0 JRNL AUTH S.KARTHIKEYAN,T.LEUNG,G.BIRRANE,G.WEBSTER,J.A.LADIAS JRNL TITL CRYSTAL STRUCTURE OF THE PDZ1 DOMAIN OF HUMAN NA(+)/H(+) JRNL TITL 2 EXCHANGER REGULATORY FACTOR PROVIDES INSIGHTS INTO THE JRNL TITL 3 MECHANISM OF CARBOXYL-TERMINAL LEUCINE RECOGNITION BY CLASS JRNL TITL 4 I PDZ DOMAINS. JRNL REF J.MOL.BIOL. V. 308 963 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11352585 JRNL DOI 10.1006/JMBI.2001.4634 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.MURTHY,C.GONZALEZ-AGOSTI,E.CORDERO,D.PINNEY,C.CANDIA, REMARK 1 AUTH 2 F.SOLOMON,J.GUSELLA,V.RAMESH REMARK 1 TITL NHE-RF, A REGULATORY COFACTOR FOR NA(+)-H+ EXCHANGE, IS A REMARK 1 TITL 2 COMMON INTERACTOR FOR MERLIN AND ERM (MERM) PROTEINS; REMARK 1 REF J.BIOL.CHEM. V. 273 1273 1998 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.273.3.1273 REMARK 1 REFERENCE 2 REMARK 1 AUTH D.L.DANIELS,A.R.COHEN,J.M.ANDERSON,A.T.BRUNGER REMARK 1 TITL CRYSTAL STRUCTURE OF THE HCASK PDZ DOMAIN REVEALS THE REMARK 1 TITL 2 STRUCTURAL BASIS OF CLASS II PDZ DOMAIN TARGET RECOGNITION REMARK 1 REF NAT.STRUCT.BIOL. V. 5 317 1998 REMARK 1 REFN ISSN 1072-8368 REMARK 1 REFERENCE 3 REMARK 1 AUTH D.A.DOYLE,A.LEE,J.LEWIS,E.KIM,M.SHENG,R.MACKINNON REMARK 1 TITL CRYSTAL STRUCTURES OF A COMPLEXED AND PEPTIDE-FREE MEMBRANE REMARK 1 TITL 2 PROTEIN-BINDING DOMAIN:MOLECULAR BASIS OF PEPTIDE REMARK 1 TITL 3 RECOGNITION BY PDZ REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 85 1067 1996 REMARK 1 REFN ISSN 0092-8674 REMARK 1 DOI 10.1016/S0092-8674(00)81307-0 REMARK 1 REFERENCE 4 REMARK 1 AUTH J.H.MORAIS CABRAL,C.PETOSA,M.J.SUTCLIFFE,S.RAZA,O.BYRON, REMARK 1 AUTH 2 F.POY,S.M.MARFATIA,A.H.CHISHTI,R.C.LIDDINGTON REMARK 1 TITL CRYSTAL STRUCTURE OF A PDZ DOMAIN REMARK 1 REF NATURE V. 382 649 1996 REMARK 1 REFN ISSN 0028-0836 REMARK 1 DOI 10.1038/382649A0 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 14816 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1500 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2154 REMARK 3 BIN R VALUE (WORKING SET) : 0.1890 REMARK 3 BIN FREE R VALUE : 0.2320 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 236 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 697 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 144 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.23000 REMARK 3 B22 (A**2) : 0.23000 REMARK 3 B33 (A**2) : -0.46000 REMARK 3 B12 (A**2) : 0.21000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : 0.06 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.08 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.080 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.820 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.370 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.210 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.810 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.41 REMARK 3 BSOL : 63.19 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN_REP.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1G9O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-00. REMARK 100 THE DEPOSITION ID IS D_1000012407. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98401 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : DUAL SLITS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14916 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 36.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : 3.90000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.15200 REMARK 200 R SYM FOR SHELL (I) : 15.2000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 10.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM SODIUM TARTRATE, SODIUM REMARK 280 CITRATE, AMMONIUM SULFATE, MANGANESE CHLORIDE, PH 5.9, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 39.29800 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 19.64900 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 19.64900 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 39.29800 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 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 ARG A 9 CB CG CD NE CZ NH1 NH2 DBREF 1G9O A 11 99 UNP O14745 NHERF_HUMAN 11 99 SEQADV 1G9O ARG A 9 UNP O14745 CLONING ARTIFACT SEQADV 1G9O MET A 10 UNP O14745 CLONING ARTIFACT SEQRES 1 A 91 ARG 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 THR ASP GLU GLN LEU FORMUL 2 HOH *144(H2 O) HELIX 1 1 SER A 46 ALA A 51 1 6 HELIX 2 2 THR A 71 ALA A 81 1 11 SHEET 1 A 4 ARG A 13 GLU A 18 0 SHEET 2 A 4 ALA A 85 VAL A 91 -1 O VAL A 86 N LEU A 17 SHEET 3 A 4 ARG A 58 VAL A 62 -1 N ARG A 58 O VAL A 91 SHEET 4 A 4 GLU A 65 ASN A 66 -1 O GLU A 65 N VAL A 62 SHEET 1 B 2 PHE A 26 GLY A 30 0 SHEET 2 B 2 GLN A 37 VAL A 42 -1 N TYR A 38 O HIS A 29 CRYST1 51.568 51.568 58.947 90.00 90.00 120.00 P 32 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 0.019392 0.011196 0.000000 0.00000 SCALE2 0.000000 0.022392 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016964 0.00000