HEADER PROTEIN BINDING 29-SEP-15 5E11 TITLE SECOND PDZ DOMAIN OF LIGAND OF NUMB PROTEIN X 2 BY LAUE TITLE 2 CRYSTALLOGRAPHY (NO ELECTRIC FIELD) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIGAND OF NUMB PROTEIN X 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SECOND PDZ DOMAIN (UNP RESIDUES 336-424); COMPND 5 SYNONYM: NUMB-BINDING PROTEIN 2,PDZ DOMAIN-CONTAINING RING FINGER COMPND 6 PROTEIN 1; COMPND 7 ENGINEERED: YES; COMPND 8 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: LNX2, PDZRN1; 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: PNIC28 KEYWDS UNPERTURBED, OFF STATE., PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR D.R.HEKSTRA,K.I.WHITE,M.A.SOCOLICH,R.W.HENNING,V.SRAJER,R.RANGANATHAN REVDAT 4 06-MAR-24 5E11 1 REMARK REVDAT 3 22-NOV-17 5E11 1 REMARK REVDAT 2 11-JAN-17 5E11 1 JRNL REVDAT 1 07-DEC-16 5E11 0 JRNL AUTH D.R.HEKSTRA,K.I.WHITE,M.A.SOCOLICH,R.W.HENNING,V.SRAJER, JRNL AUTH 2 R.RANGANATHAN JRNL TITL ELECTRIC-FIELD-STIMULATED PROTEIN MECHANICS. JRNL REF NATURE V. 540 400 2016 JRNL REFN ESSN 1476-4687 JRNL PMID 27926732 JRNL DOI 10.1038/NATURE20571 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.280 REMARK 3 COMPLETENESS FOR RANGE (%) : 78.9 REMARK 3 NUMBER OF REFLECTIONS : 6565 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.133 REMARK 3 R VALUE (WORKING SET) : 0.132 REMARK 3 FREE R VALUE : 0.148 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 328 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 30.0804 - 2.2633 0.94 3739 195 0.1342 0.1559 REMARK 3 2 2.2633 - 1.7965 0.64 2498 133 0.1245 0.1290 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.49 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 : 0.020 840 REMARK 3 ANGLE : 1.630 1142 REMARK 3 CHIRALITY : 0.102 136 REMARK 3 PLANARITY : 0.009 154 REMARK 3 DIHEDRAL : 13.172 326 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 5E11 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000214099. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 289 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : L REMARK 200 WAVELENGTH OR RANGE (A) : 1.02-1.16 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : U23 AND U27; KB MIRROR SYSTEM REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX340-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PRECOGNITION, EPINORM REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6565 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 79.3 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 34.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: LAUE REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: SSRL STRUCTURE AT 277 K (TO BE DEPOSITED) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27-31% PEG 300, 48 MM CITRIC ACID, 35 REMARK 280 MM NAH2PO4, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 32.65000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.72500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.65000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.72500 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 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 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 LYS A 396 CE NZ REMARK 470 GLU A 401 CD OE1 OE2 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 512 O HOH A 538 0.49 REMARK 500 NH1 ARG A 413 O HOH A 501 2.02 REMARK 500 NE2 GLN A 350 O HOH A 502 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 548 O HOH A 588 3546 2.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 394 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES 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 A 594 DISTANCE = 6.86 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VWR RELATED DB: PDB REMARK 900 PREVIOUS X-RAY STRUCTURE AT 100 K DETERMINED BY THE STRUCTURAL REMARK 900 GENOMICS CONSORTIUM, USING THE SAME CONSTRUCT. REMARK 900 RELATED ID: 5E1Y RELATED DB: PDB REMARK 900 RELATED ID: 5E21 RELATED DB: PDB REMARK 900 RELATED ID: 5E22 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT THE C-TERMINAL EXTENSION (RESIDUES 425-428) REMARK 999 CONTAINS A PUTATIVE LIGAND MOTIF. DBREF 5E11 A 336 424 UNP Q8N448 LNX2_HUMAN 336 424 SEQADV 5E11 SER A 334 UNP Q8N448 EXPRESSION TAG SEQADV 5E11 MET A 335 UNP Q8N448 EXPRESSION TAG SEQADV 5E11 LEU A 338 UNP Q8N448 PHE 338 ENGINEERED MUTATION SEQADV 5E11 GLU A 425 UNP Q8N448 SEE REMARK 999 SEQADV 5E11 ILE A 426 UNP Q8N448 SEE REMARK 999 SEQADV 5E11 GLU A 427 UNP Q8N448 SEE REMARK 999 SEQADV 5E11 LEU A 428 UNP Q8N448 SEE REMARK 999 SEQRES 1 A 95 SER MET GLU ILE LEU GLN VAL ALA LEU HIS LYS ARG ASP SEQRES 2 A 95 SER GLY GLU GLN LEU GLY ILE LYS LEU VAL ARG ARG THR SEQRES 3 A 95 ASP GLU PRO GLY VAL PHE ILE LEU ASP LEU LEU GLU GLY SEQRES 4 A 95 GLY LEU ALA ALA GLN ASP GLY ARG LEU SER SER ASN ASP SEQRES 5 A 95 ARG VAL LEU ALA ILE ASN GLY HIS ASP LEU LYS TYR GLY SEQRES 6 A 95 THR PRO GLU LEU ALA ALA GLN ILE ILE GLN ALA SER GLY SEQRES 7 A 95 GLU ARG VAL ASN LEU THR ILE ALA ARG PRO GLY LYS PRO SEQRES 8 A 95 GLU ILE GLU LEU FORMUL 2 HOH *94(H2 O) HELIX 1 AA1 GLY A 373 GLY A 379 1 7 HELIX 2 AA2 THR A 399 ALA A 409 1 11 SHEET 1 AA1 5 MET A 335 HIS A 343 0 SHEET 2 AA1 5 ARG A 413 PRO A 421 -1 O LEU A 416 N VAL A 340 SHEET 3 AA1 5 ARG A 386 ILE A 390 -1 N ARG A 386 O ALA A 419 SHEET 4 AA1 5 VAL A 364 LEU A 369 -1 N VAL A 364 O VAL A 387 SHEET 5 AA1 5 ILE A 353 VAL A 356 -1 N LYS A 354 O LEU A 367 SHEET 1 AA2 4 MET A 335 HIS A 343 0 SHEET 2 AA2 4 ARG A 413 PRO A 421 -1 O LEU A 416 N VAL A 340 SHEET 3 AA2 4 ARG A 386 ILE A 390 -1 N ARG A 386 O ALA A 419 SHEET 4 AA2 4 HIS A 393 ASP A 394 -1 O HIS A 393 N ILE A 390 CRYST1 65.300 39.450 39.010 90.00 117.54 90.00 C 1 2 1 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 0.015314 0.000000 0.007986 0.00000 SCALE2 0.000000 0.025349 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028910 0.00000