PDB Short entry for 4NXR HEADER SIGNALING PROTEIN/PEPTIDE 09-DEC-13 4NXR TITLE CRYSTAL STRUCTURE OF T-CELL LYMPHOMA INVASION AND METASTASIS-1 PDZ TITLE 2 DOMAIN QUADRUPLE MUTANT (QM) IN COMPLEX WITH NEUREXIN-1 PEPTIDE 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; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: NEUREXIN-2-BETA PEPTIDE; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUE 659-666; COMPND 12 SYNONYM: NEUREXIN II-BETA PEPTIDE; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 STRAIN: HUMAN; SOURCE 6 GENE: TIAM1; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET21A-6HIS-RTEV; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606 KEYWDS BETA BARREL FOLD PROTEIN, PDZ DOMAIN, PEPTIDE BINDING, SPECIFICITY KEYWDS 2 MUTANT, SCAFFOLD SIGNALING PROTEIN FOR CELL ADHESION AND CELL KEYWDS 3 JUNCTION, SIGNALING DOMAIN, SIGNALING PROTEIN-PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.LIU,D.C.SPECKHARD,T.R.SHEPHERD,S.R.HENGEL,E.J.FUENTES REVDAT 4 20-SEP-23 4NXR 1 REMARK REVDAT 3 21-DEC-22 4NXR 1 REMARK SEQADV REVDAT 2 15-FEB-17 4NXR 1 JRNL REVDAT 1 13-MAY-15 4NXR 0 JRNL AUTH X.LIU,D.C.SPECKHARD,T.R.SHEPHERD,Y.J.SUN,S.R.HENGEL,L.YU, JRNL AUTH 2 C.A.FOWLER,L.GAKHAR,E.J.FUENTES JRNL TITL DISTINCT ROLES FOR CONFORMATIONAL DYNAMICS IN PROTEIN-LIGAND JRNL TITL 2 INTERACTIONS. JRNL REF STRUCTURE V. 24 2053 2016 JRNL REFN ISSN 0969-2126 JRNL PMID 27998539 JRNL DOI 10.1016/J.STR.2016.08.019 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.640 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 6821 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.560 REMARK 3 FREE R VALUE TEST SET COUNT : 311 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 39.0661 - 3.0157 1.00 2981 150 0.1320 0.1459 REMARK 3 2 3.0157 - 2.3938 1.00 2953 140 0.1630 0.2248 REMARK 3 3 2.3938 - 2.0912 1.00 2998 151 0.1532 0.2427 REMARK 3 4 2.0912 - 1.9000 0.96 2881 124 0.1537 0.2334 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.40 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 : 0.008 832 REMARK 3 ANGLE : 1.157 1118 REMARK 3 CHIRALITY : 0.045 120 REMARK 3 PLANARITY : 0.005 142 REMARK 3 DIHEDRAL : 14.309 312 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 4NXR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000083788. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NOIR-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6821 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 39.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 39.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.03500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 11.00 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 3KZD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, 0.1M HEPES, REMARK 280 PH=7.5, 22% PEG 4000, PH 6.8, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 13.17900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.97100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.16150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.97100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.17900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.16150 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: 1640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 N ASN B 1 S ANS B 100 1.51 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 MET A 839 -76.78 -111.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 ANS B 100 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANS B 100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KZD RELATED DB: PDB REMARK 900 THE T-CELL LYMPHOMA INVASION AND METASTASIS-1 PDZ DOMAIN WILD TYPE REMARK 900 IN APO STATE REMARK 900 RELATED ID: 3KZE RELATED DB: PDB REMARK 900 THE T-CELL LYMPHOMA INVASION AND METASTASIS-1 PDZ DOMAIN WILD TYPE REMARK 900 IN MODEL PEPTIDE-BOUND STATE REMARK 900 RELATED ID: 4GVD RELATED DB: PDB REMARK 900 THE T-CELL LYMPHOMA INVASION AND METASTASIS-1 PDZ DOMAIN WILD TYPE REMARK 900 IN SDC1-BOUND STATE REMARK 900 RELATED ID: 4GVC RELATED DB: PDB REMARK 900 THE T-CELL LYMPHOMA INVASION AND METASTASIS-1 PDZ DOMAIN WILD TYPE REMARK 900 IN PSDC1-BOUND STATE REMARK 900 RELATED ID: 4NXQ RELATED DB: PDB REMARK 900 RELATED ID: 4NXP RELATED DB: PDB DBREF 4NXR A 841 930 UNP Q13009 TIAM1_HUMAN 841 930 DBREF 4NXR B 1 8 UNP P58401 NRX2B_HUMAN 659 666 SEQADV 4NXR GLY A 837 UNP Q13009 EXPRESSION TAG SEQADV 4NXR ALA A 838 UNP Q13009 EXPRESSION TAG SEQADV 4NXR MET A 839 UNP Q13009 EXPRESSION TAG SEQADV 4NXR GLY A 840 UNP Q13009 EXPRESSION TAG SEQADV 4NXR HIS A 844 UNP Q13009 GLN 844 VARIANT SEQADV 4NXR MET A 911 UNP Q13009 LEU 911 ENGINEERED MUTATION SEQADV 4NXR GLU A 912 UNP Q13009 LYS 912 ENGINEERED MUTATION SEQADV 4NXR PHE A 915 UNP Q13009 LEU 915 ENGINEERED MUTATION SEQADV 4NXR VAL A 920 UNP Q13009 LEU 920 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 MET GLU ASP PHE SEQRES 7 A 94 PHE SER GLN PRO SER VAL GLY LEU LEU VAL ARG THR TYR SEQRES 8 A 94 PRO GLU LEU SEQRES 1 B 8 ASN LYS ASP LYS GLU TYR TYR VAL HET EPE A1001 15 HET ANS B 100 16 HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM ANS 5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL HETNAM 2 ANS ACID) HETSYN EPE HEPES HETSYN ANS DANSYL ACID FORMUL 3 EPE C8 H18 N2 O4 S FORMUL 4 ANS C12 H13 N O3 S FORMUL 5 HOH *99(H2 O) HELIX 1 1 SER A 851 THR A 853 5 3 HELIX 2 2 GLY A 882 LYS A 887 1 6 HELIX 3 3 ASP A 904 LEU A 906 5 3 HELIX 4 4 ASN A 907 GLN A 917 1 11 SHEET 1 A 4 VAL A 842 GLU A 849 0 SHEET 2 A 4 SER A 919 THR A 926 -1 O THR A 926 N VAL A 842 SHEET 3 A 4 GLU A 894 ILE A 898 -1 N GLU A 894 O ARG A 925 SHEET 4 A 4 ARG A 901 ALA A 902 -1 O ARG A 901 N ILE A 898 SHEET 1 B 3 ILE A 870 ASN A 876 0 SHEET 2 B 3 SER A 861 GLU A 867 -1 N SER A 861 O ASN A 876 SHEET 3 B 3 LYS B 2 TYR B 7 -1 O LYS B 4 N SER A 864 SITE 1 AC1 12 ALA A 838 ASP A 868 GLY A 869 LYS A 879 SITE 2 AC1 12 GLU A 897 ASN A 900 TYR A 927 HOH A1146 SITE 3 AC1 12 HOH A1161 HOH A1181 TYR B 7 HOH B 203 SITE 1 AC2 6 ARG A 901 ASN A 907 SER A 909 ASP A 913 SITE 2 AC2 6 PHE A 914 ASN B 1 CRYST1 26.358 50.323 61.942 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 0.037939 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019872 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016144 0.00000