HEADER SIGNALING PROTEIN 08-DEC-09 3KZD TITLE CRYSTAL STRUCTURE OF FREE T-CELL LYMPHOMA INVASION AND METASTASIS-1 TITLE 2 PDZ DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-LYMPHOMA INVASION AND METASTASIS-INDUCING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ DOMAIN; COMPND 5 SYNONYM: TIAM-1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TIAM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A-6HIS-RTEV KEYWDS PDZ, CELL JUNCTION, CELL ADHESION, SIGNALING PROTEIN, TIAM1, GUANINE KEYWDS 2 NUCLEOTIDE EXCHANGE FACTOR, GUANINE-NUCLEOTIDE RELEASING FACTOR, KEYWDS 3 LIPOPROTEIN, MYRISTATE, PHOSPHOPROTEIN, POLYMORPHISM EXPDTA X-RAY DIFFRACTION AUTHOR T.R.SHEPHERD,E.J.FUENTES REVDAT 5 21-FEB-24 3KZD 1 REMARK REVDAT 4 13-OCT-21 3KZD 1 SEQADV REVDAT 3 01-NOV-17 3KZD 1 REMARK REVDAT 2 19-MAY-10 3KZD 1 JRNL REVDAT 1 21-APR-10 3KZD 0 JRNL AUTH T.R.SHEPHERD,S.M.KLAUS,X.LIU,S.RAMASWAMY,K.A.DEMALI, JRNL AUTH 2 E.J.FUENTES JRNL TITL THE TIAM1 PDZ DOMAIN COUPLES TO SYNDECAN1 AND PROMOTES JRNL TITL 2 CELL-MATRIX ADHESION. JRNL REF J.MOL.BIOL. V. 398 730 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20361982 JRNL DOI 10.1016/J.JMB.2010.03.047 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.5_2 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 20510 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2009 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 34.0250 - 3.1290 0.97 1409 152 0.2030 0.2000 REMARK 3 2 3.1290 - 2.4840 0.99 1363 149 0.2070 0.2580 REMARK 3 3 2.4840 - 2.1700 1.00 1360 151 0.1880 0.2280 REMARK 3 4 2.1700 - 1.9720 1.00 1338 146 0.1710 0.1690 REMARK 3 5 1.9720 - 1.8310 0.99 1343 146 0.1700 0.2290 REMARK 3 6 1.8310 - 1.7220 0.99 1299 139 0.1720 0.2240 REMARK 3 7 1.7220 - 1.6360 0.99 1345 151 0.1730 0.2080 REMARK 3 8 1.6360 - 1.5650 0.98 1294 135 0.1560 0.1980 REMARK 3 9 1.5650 - 1.5050 0.99 1304 143 0.1550 0.2040 REMARK 3 10 1.5050 - 1.4530 0.98 1321 145 0.1520 0.1900 REMARK 3 11 1.4530 - 1.4070 0.98 1272 135 0.1570 0.2010 REMARK 3 12 1.4070 - 1.3670 0.98 1288 142 0.1560 0.2190 REMARK 3 13 1.3670 - 1.3310 0.97 1292 141 0.1630 0.2180 REMARK 3 14 1.3310 - 1.3000 0.96 1273 134 0.1710 0.2220 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 : 0.45 REMARK 3 B_SOL : 49.75 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.96900 REMARK 3 B22 (A**2) : 0.96900 REMARK 3 B33 (A**2) : -2.84500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.005 696 REMARK 3 ANGLE : 0.995 952 REMARK 3 CHIRALITY : 0.065 114 REMARK 3 PLANARITY : 0.004 122 REMARK 3 DIHEDRAL : 14.597 266 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 3KZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056637. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03320 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYO-COOLED REMARK 200 SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK 9.9L REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20526 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 34.025 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 10.25 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.33600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.3.3, MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 3350, 0.2 M NASCN, PH REMARK 280 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 288K 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 47.19933 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 23.59967 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 23.59967 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 47.19933 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 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 837 REMARK 465 ALA A 838 REMARK 465 MET A 839 REMARK 465 SER A 851 REMARK 465 ASP A 852 REMARK 465 THR A 853 REMARK 465 ALA A 854 REMARK 465 ALA A 855 REMARK 465 ASP A 856 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 GLU A 866 CG CD OE1 OE2 REMARK 470 GLU A 867 CG CD OE1 OE2 REMARK 470 LYS A 879 CD CE NZ REMARK 470 GLU A 880 CD OE1 OE2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KZE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF T-CELL LYMPHOMA INVASION AND METASTASIS-1 PDZ REMARK 900 IN COMPLEX WITH SSRKEYYA PEPTIDE DBREF 3KZD A 841 930 UNP Q13009 TIAM1_HUMAN 841 930 SEQADV 3KZD GLY A 837 UNP Q13009 EXPRESSION TAG SEQADV 3KZD ALA A 838 UNP Q13009 EXPRESSION TAG SEQADV 3KZD MET A 839 UNP Q13009 EXPRESSION TAG SEQADV 3KZD GLY A 840 UNP Q13009 EXPRESSION TAG SEQADV 3KZD HIS A 844 UNP Q13009 GLN 844 ENGINEERED MUTATION SEQRES 1 A 94 GLY ALA MET GLY LYS VAL THR HIS SER ILE HIS ILE GLU SEQRES 2 A 94 LYS SER ASP THR ALA ALA ASP THR TYR GLY PHE SER LEU SEQRES 3 A 94 SER SER VAL GLU GLU ASP GLY ILE ARG ARG LEU TYR VAL SEQRES 4 A 94 ASN SER VAL LYS GLU THR GLY LEU ALA SER LYS LYS GLY SEQRES 5 A 94 LEU LYS ALA GLY ASP GLU ILE LEU GLU ILE ASN ASN ARG SEQRES 6 A 94 ALA ALA ASP ALA LEU ASN SER SER MET LEU LYS ASP PHE SEQRES 7 A 94 LEU SER GLN PRO SER LEU GLY LEU LEU VAL ARG THR TYR SEQRES 8 A 94 PRO GLU LEU FORMUL 2 HOH *75(H2 O) HELIX 1 1 GLY A 882 LYS A 887 1 6 HELIX 2 2 ASP A 904 LEU A 906 5 3 HELIX 3 3 ASN A 907 GLN A 917 1 11 SHEET 1 A 5 VAL A 842 GLU A 849 0 SHEET 2 A 5 SER A 919 THR A 926 -1 O VAL A 924 N HIS A 844 SHEET 3 A 5 GLU A 894 ILE A 898 -1 N GLU A 894 O ARG A 925 SHEET 4 A 5 ARG A 872 VAL A 878 -1 N LEU A 873 O ILE A 895 SHEET 5 A 5 PHE A 860 VAL A 865 -1 N VAL A 865 O ARG A 872 SHEET 1 B 4 VAL A 842 GLU A 849 0 SHEET 2 B 4 SER A 919 THR A 926 -1 O VAL A 924 N HIS A 844 SHEET 3 B 4 GLU A 894 ILE A 898 -1 N GLU A 894 O ARG A 925 SHEET 4 B 4 ARG A 901 ALA A 902 -1 O ARG A 901 N ILE A 898 CRYST1 44.782 44.782 70.799 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 0.022330 0.012892 0.000000 0.00000 SCALE2 0.000000 0.025785 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014125 0.00000