HEADER METAL BINDING PROTEIN/APOTOSIS 24-MAY-16 5B5W TITLE CRYSTAL STRUCTURE OF MOB1-LATS1 NTR DOMAIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: MOB KINASE ACTIVATOR 1B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 33-216; COMPND 5 SYNONYM: MOB1 HOMOLOG 1A,MPS ONE BINDER KINASE ACTIVATOR-LIKE 1A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: SERINE/THREONINE-PROTEIN KINASE LATS1; COMPND 9 CHAIN: U; COMPND 10 FRAGMENT: UNP RESIDUES 622-704; COMPND 11 SYNONYM: LARGE TUMOR SUPPRESSOR HOMOLOG 1,WARTS PROTEIN KINASE,H- COMPND 12 WARTS; COMPND 13 EC: 2.7.11.1; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: MOB1B, MOBKL1A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: LATS1, WARTS; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MOB1 LATS1 HIPPO PATHWAY, METAL BINDING PROTEIN-APOTOSIS COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.-Y.KIM,Y.TACHIOKA,T.MORI,T.HAKOSHIMA REVDAT 3 08-NOV-23 5B5W 1 REMARK REVDAT 2 26-FEB-20 5B5W 1 REMARK REVDAT 1 06-JUL-16 5B5W 0 JRNL AUTH S.Y.KIM,Y.TACHIOKA,T.MORI,T.HAKOSHIMA JRNL TITL STRUCTURAL BASIS FOR AUTOINHIBITION AND ITS RELIEF OF MOB1 JRNL TITL 2 IN THE HIPPO PATHWAY JRNL REF SCI REP V. 6 28488 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27335147 JRNL DOI 10.1038/SREP28488 REMARK 2 REMARK 2 RESOLUTION. 2.96 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 6109 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.700 REMARK 3 FREE R VALUE TEST SET COUNT : 348 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 28.2977 - 3.7242 0.97 3075 207 0.2115 0.2503 REMARK 3 2 3.7242 - 2.9570 0.85 2686 141 0.3226 0.3695 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.003 2018 REMARK 3 ANGLE : 0.745 2709 REMARK 3 CHIRALITY : 0.027 286 REMARK 3 PLANARITY : 0.003 349 REMARK 3 DIHEDRAL : 14.642 767 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 5B5W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1300000592. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6660 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.957 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-2000 REMARK 200 STARTING MODEL: 1PI1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277K 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 39.37350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.88000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.37350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.88000 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: 2480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, U 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 31 REMARK 465 PRO A 32 REMARK 465 GLU A 33 REMARK 465 ALA A 34 REMARK 465 THR A 35 REMARK 465 LEU A 36 REMARK 465 GLY A 37 REMARK 465 SER A 38 REMARK 465 THR A 101 REMARK 465 ASN A 102 REMARK 465 ILE A 103 REMARK 465 LYS A 214 REMARK 465 ASP A 215 REMARK 465 ARG A 216 REMARK 465 GLY U 619 REMARK 465 PRO U 620 REMARK 465 LYS U 621 REMARK 465 ASP U 622 REMARK 465 GLU U 623 REMARK 465 GLU U 624 REMARK 465 ARG U 625 REMARK 465 ARG U 626 REMARK 465 GLU U 627 REMARK 465 SER U 628 REMARK 465 ARG U 629 REMARK 465 ILE U 630 REMARK 465 GLN U 631 REMARK 465 SER U 632 REMARK 465 TYR U 633 REMARK 465 SER U 634 REMARK 465 MET U 699 REMARK 465 ASP U 700 REMARK 465 LYS U 701 REMARK 465 SER U 702 REMARK 465 MET U 703 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 TYR A 117 CE1 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 GLU A 81 -12.76 68.50 REMARK 500 HIS A 164 -65.44 -91.00 REMARK 500 GLN A 174 98.98 -65.61 REMARK 500 GLU A 175 -13.09 -148.72 REMARK 500 ILE A 208 -72.68 -49.29 REMARK 500 ALA U 697 -102.92 -98.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 79 SG REMARK 620 2 CYS A 84 SG 111.3 REMARK 620 3 HIS A 161 NE2 110.9 107.1 REMARK 620 4 HIS A 166 NE2 140.9 85.5 96.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5B5V RELATED DB: PDB DBREF 5B5W A 33 216 UNP Q8BPB0 MOB1B_MOUSE 33 216 DBREF 5B5W U 621 703 UNP O95835 LATS1_HUMAN 622 704 SEQADV 5B5W GLY A 31 UNP Q8BPB0 EXPRESSION TAG SEQADV 5B5W PRO A 32 UNP Q8BPB0 EXPRESSION TAG SEQADV 5B5W GLY U 619 UNP O95835 EXPRESSION TAG SEQADV 5B5W PRO U 620 UNP O95835 EXPRESSION TAG SEQRES 1 A 186 GLY PRO GLU ALA THR LEU GLY SER GLY ASN LEU ARG MET SEQRES 2 A 186 ALA VAL MET LEU PRO GLU GLY GLU ASP LEU ASN GLU TRP SEQRES 3 A 186 VAL ALA VAL ASN THR VAL ASP PHE PHE ASN GLN ILE ASN SEQRES 4 A 186 MET LEU TYR GLY THR ILE THR ASP PHE CYS THR GLU GLU SEQRES 5 A 186 SER CYS PRO VAL MET SER ALA GLY PRO LYS TYR GLU TYR SEQRES 6 A 186 HIS TRP ALA ASP GLY THR ASN ILE LYS LYS PRO ILE LYS SEQRES 7 A 186 CYS SER ALA PRO LYS TYR ILE ASP TYR LEU MET THR TRP SEQRES 8 A 186 VAL GLN ASP GLN LEU ASP ASP GLU THR LEU PHE PRO SER SEQRES 9 A 186 LYS ILE GLY VAL PRO PHE PRO LYS ASN PHE MET SER VAL SEQRES 10 A 186 ALA LYS THR ILE LEU LYS ARG LEU PHE ARG VAL TYR ALA SEQRES 11 A 186 HIS ILE TYR HIS GLN HIS PHE ASP PRO VAL ILE GLN LEU SEQRES 12 A 186 GLN GLU GLU ALA HIS LEU ASN THR SER PHE LYS HIS PHE SEQRES 13 A 186 ILE PHE PHE VAL GLN GLU PHE ASN LEU ILE ASP ARG ARG SEQRES 14 A 186 GLU LEU ALA PRO LEU GLN GLU LEU ILE GLU LYS LEU THR SEQRES 15 A 186 SER LYS ASP ARG SEQRES 1 U 85 GLY PRO LYS ASP GLU GLU ARG ARG GLU SER ARG ILE GLN SEQRES 2 U 85 SER TYR SER PRO GLN ALA PHE LYS PHE PHE MET GLU GLN SEQRES 3 U 85 HIS VAL GLU ASN VAL LEU LYS SER HIS GLN GLN ARG LEU SEQRES 4 U 85 HIS ARG LYS LYS GLN LEU GLU ASN GLU MET MET ARG VAL SEQRES 5 U 85 GLY LEU SER GLN ASP ALA GLN ASP GLN MET ARG LYS MET SEQRES 6 U 85 LEU CYS GLN LYS GLU SER ASN TYR ILE ARG LEU LYS ARG SEQRES 7 U 85 ALA LYS MET ASP LYS SER MET HET ZN A 301 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ HELIX 1 AA1 ASP A 52 THR A 76 1 25 HELIX 2 AA2 SER A 110 ASP A 128 1 19 HELIX 3 AA3 ASN A 143 HIS A 166 1 24 HELIX 4 AA4 HIS A 166 GLN A 172 1 7 HELIX 5 AA5 GLU A 175 ASN A 194 1 20 HELIX 6 AA6 ASP A 197 PRO A 203 5 7 HELIX 7 AA7 LEU A 204 THR A 212 1 9 HELIX 8 AA8 GLN U 636 ARG U 669 1 34 HELIX 9 AA9 SER U 673 ALA U 697 1 25 SHEET 1 AA1 2 SER A 88 ALA A 89 0 SHEET 2 AA1 2 TYR A 93 GLU A 94 -1 O TYR A 93 N ALA A 89 LINK SG CYS A 79 ZN ZN A 301 1555 1555 2.51 LINK SG CYS A 84 ZN ZN A 301 1555 1555 2.31 LINK NE2 HIS A 161 ZN ZN A 301 1555 1555 2.03 LINK NE2 HIS A 166 ZN ZN A 301 1555 1555 2.03 SITE 1 AC1 4 CYS A 79 CYS A 84 HIS A 161 HIS A 166 CRYST1 78.747 71.760 57.855 90.00 101.99 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 0.012699 0.000000 0.002697 0.00000 SCALE2 0.000000 0.013935 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017670 0.00000