HEADER SIGNALING PROTEIN 27-FEB-19 6JJY
TITLE CRYSTAL STRUCTURE OF KIBRA AND BETA-DYSTROGLYCAN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTEIN KIBRA;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: KIDNEY AND BRAIN PROTEIN,KIBRA,WW DOMAIN-CONTAINING PROTEIN
COMPND 5 1;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: PEPTIDE FROM DYSTROGLYCAN;
COMPND 9 CHAIN: U;
COMPND 10 SYNONYM: DYSTROPHIN-ASSOCIATED GLYCOPROTEIN 1;
COMPND 11 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: WWC1, KIAA0869;
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: DAG1;
SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS WW TANDEM, PY TANDEM, KIBRA, PTPN14, SIGNALING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR Z.LIN,Z.YANG,Z.JI,M.ZHANG
REVDAT 1 25-SEP-19 6JJY 0
JRNL AUTH Z.LIN,Z.YANG,R.XIE,Z.JI,K.GUAN,M.ZHANG
JRNL TITL DECODING WW DOMAIN TANDEM-MEDIATED TARGET RECOGNITIONS IN
JRNL TITL 2 TISSUE GROWTH AND CELL POLARITY.
JRNL REF ELIFE V. 8 2019
JRNL REFN ESSN 2050-084X
JRNL PMID 31486770
JRNL DOI 10.7554/ELIFE.49439
REMARK 2
REMARK 2 RESOLUTION. 2.30 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) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.57
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8
REMARK 3 NUMBER OF REFLECTIONS : 14386
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.210
REMARK 3 R VALUE (WORKING SET) : 0.206
REMARK 3 FREE R VALUE : 0.253
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1439
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 40.5776 - 4.9473 0.98 1444 159 0.1683 0.2153
REMARK 3 2 4.9473 - 3.9278 0.99 1387 153 0.1590 0.1974
REMARK 3 3 3.9278 - 3.4316 0.99 1357 153 0.1814 0.2171
REMARK 3 4 3.4316 - 3.1180 0.99 1342 149 0.2201 0.3239
REMARK 3 5 3.1180 - 2.8946 0.98 1344 150 0.2487 0.2904
REMARK 3 6 2.8946 - 2.7240 0.96 1284 140 0.2665 0.3117
REMARK 3 7 2.7240 - 2.5876 0.93 1268 133 0.2482 0.2902
REMARK 3 8 2.5876 - 2.4750 0.91 1215 136 0.2448 0.2547
REMARK 3 9 2.4750 - 2.3797 0.88 1164 135 0.2528 0.2993
REMARK 3 10 2.3797 - 2.2976 0.86 1142 131 0.2772 0.3489
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) : 0.290
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.480
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 : 0.009 1249
REMARK 3 ANGLE : 1.101 1711
REMARK 3 CHIRALITY : 0.040 174
REMARK 3 PLANARITY : 0.006 229
REMARK 3 DIHEDRAL : 15.926 467
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: ALL
REMARK 3 ORIGIN FOR THE GROUP (A): -94.2259 65.4788 127.1158
REMARK 3 T TENSOR
REMARK 3 T11: 0.3127 T22: 0.2697
REMARK 3 T33: 0.3133 T12: 0.0122
REMARK 3 T13: 0.0522 T23: 0.0342
REMARK 3 L TENSOR
REMARK 3 L11: 0.7193 L22: -0.0379
REMARK 3 L33: 2.6504 L12: 0.5142
REMARK 3 L13: -1.4105 L23: -0.6824
REMARK 3 S TENSOR
REMARK 3 S11: -0.1048 S12: -0.0338 S13: 0.0505
REMARK 3 S21: 0.1623 S22: 0.0939 S23: 0.0559
REMARK 3 S31: 0.1397 S32: -0.1175 S33: 0.0396
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 6JJY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAR-19.
REMARK 100 THE DEPOSITION ID IS D_1300011248.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 19-MAY-16
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRF
REMARK 200 BEAMLINE : BL19U1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000
REMARK 200 DATA SCALING SOFTWARE : HKL-3000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15114
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
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 (%) : 99.7
REMARK 200 DATA REDUNDANCY : 10.50
REMARK 200 R MERGE (I) : 0.05600
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 40.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 10.70
REMARK 200 R MERGE FOR SHELL (I) : 0.88600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700
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: 6J68
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 72.53
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.48
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 3.0-4.0M NACL, 100MM BIS-TRIS (PH
REMARK 280 6.5), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 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
REMARK 290 3555 -X+Y,-X,Z
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z
REMARK 290 6555 -X,-X+Y,-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 -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 0.00000
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 0.00000
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 0.00000
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 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: 1450 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 11170 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 S SO4 A 201 LIES ON A SPECIAL POSITION.
REMARK 375 O3 SO4 A 201 LIES ON A SPECIAL POSITION.
REMARK 375 S SO4 U 901 LIES ON A SPECIAL POSITION.
REMARK 375 O1 SO4 U 901 LIES ON A SPECIAL POSITION.
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 -1
REMARK 465 PRO A 0
REMARK 465 GLY A 1
REMARK 465 SER A 2
REMARK 465 GLU A 3
REMARK 465 HIS A 132
REMARK 465 GLY U 875
REMARK 465 PRO U 876
REMARK 465 GLY U 877
REMARK 465 SER U 878
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 PHE A 4 CG CD1 CD2 CE1 CE2 CZ
REMARK 470 GLU A 5 CG CD OE1 OE2
REMARK 470 ARG A 28 CG CD NE CZ NH1 NH2
REMARK 470 ARG A 40 CD NE CZ NH1 NH2
REMARK 470 ARG A 89 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 111 CG CD CE NZ
REMARK 470 ARG U 879 CG CD NE CZ NH1 NH2
REMARK 470 LYS U 881 CG CD CE NZ
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 U 901
DBREF 6JJY A 5 132 UNP Q5SXA9 KIBRA_MOUSE 5 132
DBREF 6JJY U 877 895 UNP Q14118 DAG1_HUMAN 877 895
SEQADV 6JJY GLY A -1 UNP Q5SXA9 EXPRESSION TAG
SEQADV 6JJY PRO A 0 UNP Q5SXA9 EXPRESSION TAG
SEQADV 6JJY GLY A 1 UNP Q5SXA9 EXPRESSION TAG
SEQADV 6JJY SER A 2 UNP Q5SXA9 EXPRESSION TAG
SEQADV 6JJY GLU A 3 UNP Q5SXA9 EXPRESSION TAG
SEQADV 6JJY PHE A 4 UNP Q5SXA9 EXPRESSION TAG
SEQADV 6JJY GLY U 875 UNP Q14118 EXPRESSION TAG
SEQADV 6JJY PRO U 876 UNP Q14118 EXPRESSION TAG
SEQRES 1 A 134 GLY PRO GLY SER GLU PHE GLU LEU PRO LEU PRO GLU GLY
SEQRES 2 A 134 TRP GLU GLU ALA ARG ASP PHE ASP GLY LYS VAL TYR TYR
SEQRES 3 A 134 ILE ASP HIS ARG ASN ARG THR THR SER TRP ILE ASP PRO
SEQRES 4 A 134 ARG ASP ARG TYR THR LYS PRO LEU THR PHE ALA ASP CYS
SEQRES 5 A 134 ILE SER ASP GLU LEU PRO LEU GLY TRP GLU GLU ALA TYR
SEQRES 6 A 134 ASP PRO GLN VAL GLY ASP TYR PHE ILE ASP HIS ASN THR
SEQRES 7 A 134 LYS THR THR GLN ILE GLU ASP PRO ARG VAL GLN TRP ARG
SEQRES 8 A 134 ARG GLU GLN GLU HIS MET LEU LYS ASP TYR LEU VAL VAL
SEQRES 9 A 134 ALA GLN GLU ALA LEU SER ALA GLN LYS GLU ILE TYR GLN
SEQRES 10 A 134 VAL LYS GLN GLN ARG LEU GLU LEU ALA GLN GLN GLU TYR
SEQRES 11 A 134 GLN GLN LEU HIS
SEQRES 1 U 21 GLY PRO GLY SER ARG PRO LYS ASN MET THR PRO TYR ARG
SEQRES 2 U 21 SER PRO PRO PRO TYR VAL PRO PRO
HET SO4 A 201 5
HET SO4 U 901 5
HETNAM SO4 SULFATE ION
FORMUL 3 SO4 2(O4 S 2-)
FORMUL 5 HOH *75(H2 O)
HELIX 1 AA1 ARG A 38 THR A 42 5 5
HELIX 2 AA2 THR A 46 CYS A 50 5 5
HELIX 3 AA3 ASP A 83 GLN A 129 1 47
SHEET 1 AA1 3 TRP A 12 ARG A 16 0
SHEET 2 AA1 3 VAL A 22 ASP A 26 -1 O ILE A 25 N GLU A 13
SHEET 3 AA1 3 THR A 31 SER A 33 -1 O SER A 33 N TYR A 24
SHEET 1 AA2 3 TRP A 59 ASP A 64 0
SHEET 2 AA2 3 GLY A 68 ASP A 73 -1 O GLY A 68 N ASP A 64
SHEET 3 AA2 3 THR A 78 GLN A 80 -1 O THR A 78 N ASP A 73
CISPEP 1 ILE A 51 SER A 52 0 -2.30
SITE 1 AC1 3 PRO U 891 TYR U 892 VAL U 893
CRYST1 73.483 73.483 105.322 90.00 90.00 120.00 P 3 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 0.013609 0.007857 0.000000 0.00000
SCALE2 0.000000 0.015714 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009495 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
