PDB Short entry for 4Z68 HEADER PROTEIN BINDING 04-APR-15 4Z68 TITLE HYBRID STRUCTURAL ANALYSIS OF THE ARP2/3 REGULATOR ARPIN IDENTIFIES TITLE 2 ITS ACIDIC TAIL AS A PRIMARY BINDING EPITOPE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TANKYRASE-2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ANKYRIN REPEATS DOMAIN, UNP RESIDUES 490-644; COMPND 5 SYNONYM: TANK2,ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 6,ARTD6, COMPND 6 POLY [ADP-RIBOSE] POLYMERASE 5B,TNKS-2,TRF1-INTERACTING ANKYRIN- COMPND 7 RELATED ADP-RIBOSE POLYMERASE 2,TANKYRASE II,TANKYRASE-LIKE PROTEIN, COMPND 8 TANKYRASE-RELATED PROTEIN; COMPND 9 EC: 2.4.2.30; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: GLU-ILE-ARG-GLU-GLN-GLY-ASP-GLY-ALA-GLU-ASP-GLU; COMPND 13 CHAIN: E; COMPND 14 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: TNKS2, PARP5B, TANK2, TNKL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETG30A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS CELL MIGRATION, ARPIN, ARP 2/3, ACTIN POLYMERIZATION, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.K.FETICS,V.CAMPANACCI,I.DANG,A.GAUTREAU,J.CHERFILS REVDAT 5 10-JAN-24 4Z68 1 REMARK REVDAT 4 06-SEP-17 4Z68 1 REMARK REVDAT 3 10-FEB-16 4Z68 1 JRNL REVDAT 2 27-JAN-16 4Z68 1 JRNL REVDAT 1 30-DEC-15 4Z68 0 JRNL AUTH S.FETICS,A.THUREAU,V.CAMPANACCI,M.AUMONT-NICAISE,I.DANG, JRNL AUTH 2 A.GAUTREAU,J.PEREZ,J.CHERFILS JRNL TITL HYBRID STRUCTURAL ANALYSIS OF THE ARP2/3 REGULATOR ARPIN JRNL TITL 2 IDENTIFIES ITS ACIDIC TAIL AS A PRIMARY BINDING EPITOPE. JRNL REF STRUCTURE V. 24 252 2016 JRNL REFN ISSN 0969-2126 JRNL PMID 26774128 JRNL DOI 10.1016/J.STR.2015.12.001 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 12293 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1230 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 40.5841 - 3.8662 0.99 1335 149 0.1760 0.2059 REMARK 3 2 3.8662 - 3.0690 1.00 1253 139 0.1620 0.2009 REMARK 3 3 3.0690 - 2.6812 1.00 1242 138 0.1828 0.2477 REMARK 3 4 2.6812 - 2.4361 1.00 1221 136 0.1649 0.2045 REMARK 3 5 2.4361 - 2.2615 1.00 1236 137 0.1659 0.2110 REMARK 3 6 2.2615 - 2.1281 1.00 1215 135 0.1612 0.2102 REMARK 3 7 2.1281 - 2.0216 1.00 1217 135 0.1679 0.2227 REMARK 3 8 2.0216 - 1.9336 1.00 1202 135 0.1677 0.2545 REMARK 3 9 1.9336 - 1.8591 0.96 1142 126 0.1703 0.2516 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 43.01 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.36020 REMARK 3 B22 (A**2) : 4.99730 REMARK 3 B33 (A**2) : -0.63700 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 : 0.006 1307 REMARK 3 ANGLE : 1.041 1780 REMARK 3 CHIRALITY : 0.067 202 REMARK 3 PLANARITY : 0.005 236 REMARK 3 DIHEDRAL : 14.675 470 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 4Z68 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208682. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12297 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.859 REMARK 200 RESOLUTION RANGE LOW (A) : 40.574 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.000 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: 3TWR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, ISOPROPANOL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, 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 14.77150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.81850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.90300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.81850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.77150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.90300 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: 1500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E 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 GLU A 491 CG CD OE1 OE2 REMARK 470 ARG A 494 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 509 CG CD CE NZ REMARK 470 LYS A 510 CG CD CE NZ REMARK 470 ILE A 522 CG1 CG2 CD1 REMARK 470 GLU A 523 CG CD OE1 OE2 REMARK 470 GLN A 547 CG CD OE1 NE2 REMARK 470 GLU A 576 OE1 REMARK 470 LYS A 580 CG CD CE NZ REMARK 470 ASP A 638 CG OD1 OD2 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 PRO A 618 O HOH A 801 2.16 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 857 O HOH A 861 1455 2.15 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 863 DISTANCE = 6.30 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 702 DBREF 4Z68 A 490 644 UNP Q9H2K2 TNKS2_HUMAN 490 644 DBREF 4Z68 E 211 222 PDB 4Z68 4Z68 211 222 SEQRES 1 A 155 SER GLU ALA ASP ARG GLN LEU LEU GLU ALA ALA LYS ALA SEQRES 2 A 155 GLY ASP VAL GLU THR VAL LYS LYS LEU CYS THR VAL GLN SEQRES 3 A 155 SER VAL ASN CYS ARG ASP ILE GLU GLY ARG GLN SER THR SEQRES 4 A 155 PRO LEU HIS PHE ALA ALA GLY TYR ASN ARG VAL SER VAL SEQRES 5 A 155 VAL GLU TYR LEU LEU GLN HIS GLY ALA ASP VAL HIS ALA SEQRES 6 A 155 LYS ASP LYS GLY GLY LEU VAL PRO LEU HIS ASN ALA CYS SEQRES 7 A 155 SER TYR GLY HIS TYR GLU VAL ALA GLU LEU LEU VAL LYS SEQRES 8 A 155 HIS GLY ALA VAL VAL ASN VAL ALA ASP LEU TRP LYS PHE SEQRES 9 A 155 THR PRO LEU HIS GLU ALA ALA ALA LYS GLY LYS TYR GLU SEQRES 10 A 155 ILE CYS LYS LEU LEU LEU GLN HIS GLY ALA ASP PRO THR SEQRES 11 A 155 LYS LYS ASN ARG ASP GLY ASN THR PRO LEU ASP LEU VAL SEQRES 12 A 155 LYS ASP GLY ASP THR ASP ILE GLN ASP LEU LEU ARG SEQRES 1 E 12 GLU ILE ARG GLU GLN GLY ASP GLY ALA GLU ASP GLU HET SO4 A 701 5 HET SO4 A 702 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *68(H2 O) HELIX 1 AA1 SER A 490 GLY A 503 1 14 HELIX 2 AA2 ASP A 504 CYS A 512 1 9 HELIX 3 AA3 GLN A 515 CYS A 519 5 5 HELIX 4 AA4 THR A 528 TYR A 536 1 9 HELIX 5 AA5 ARG A 538 HIS A 548 1 11 HELIX 6 AA6 VAL A 561 TYR A 569 1 9 HELIX 7 AA7 HIS A 571 HIS A 581 1 11 HELIX 8 AA8 THR A 594 GLY A 603 1 10 HELIX 9 AA9 LYS A 604 HIS A 614 1 11 HELIX 10 AB1 THR A 627 VAL A 632 1 6 HELIX 11 AB2 ASP A 636 LEU A 643 1 8 SITE 1 AC1 7 ASN A 537 ARG A 538 VAL A 539 SER A 540 SITE 2 AC1 7 LYS A 557 HOH A 802 HOH A 814 SITE 1 AC2 4 GLU A 576 LYS A 592 HIS A 614 ARG A 623 CRYST1 29.543 43.806 107.637 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 0.033849 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022828 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009290 0.00000