PDB Short entry for 4YL6 HEADER PROTEIN BINDING 05-MAR-15 4YL6 TITLE CRYSTAL STRUCTURE OF TRUNCATED CEREBRAL CAVERNOUS MALFORMATION 2 C- TITLE 2 TERMINAL ADAPTOR DOMAIN IN COMPLEX WITH AN INTERNAL HELIX OF MITOGEN- TITLE 3 ACTIVATED PROTEIN KINASE KINASE KINASE 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALCAVERNIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TRUNCATED FRAGMENT OF C-TERMINAL ADAPTOR DOMAIN, UNP COMPND 5 RESIDUES 290-376; COMPND 6 SYNONYM: CEREBRAL CAVERNOUS MALFORMATIONS 2 PROTEIN; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 3; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 1-22; COMPND 12 SYNONYM: MAPK/ERK KINASE KINASE 3,MEKK 3; 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 GENE: CCM2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); 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: PET22B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS ADAPTOR-PARTNER COMPLEX, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.DING,X.WANG,D.C.WANG REVDAT 3 08-NOV-23 4YL6 1 SOURCE JRNL REMARK REVDAT 2 17-JUN-15 4YL6 1 JRNL REVDAT 1 03-JUN-15 4YL6 0 JRNL AUTH X.WANG,Y.HOU,K.DENG,Y.ZHANG,D.C.WANG,J.DING JRNL TITL STRUCTURAL INSIGHTS INTO THE MOLECULAR RECOGNITION BETWEEN JRNL TITL 2 CEREBRAL CAVERNOUS MALFORMATION 2 AND MITOGEN-ACTIVATED JRNL TITL 3 PROTEIN KINASE KINASE KINASE 3 JRNL REF STRUCTURE V. 23 1087 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 25982527 JRNL DOI 10.1016/J.STR.2015.04.003 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 8036 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 370 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 45.7946 - 3.0285 1.00 2693 122 0.2016 0.2290 REMARK 3 2 3.0285 - 2.4039 1.00 2533 123 0.2051 0.2341 REMARK 3 3 2.4039 - 2.1000 0.98 2440 125 0.2064 0.2702 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.11 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 40.95 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.21160 REMARK 3 B22 (A**2) : -4.21160 REMARK 3 B33 (A**2) : 8.42330 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 : 0.002 870 REMARK 3 ANGLE : 0.636 1170 REMARK 3 CHIRALITY : 0.040 133 REMARK 3 PLANARITY : 0.002 152 REMARK 3 DIHEDRAL : 13.001 328 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 4YL6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207605. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8073 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 45.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.29800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.900 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: 4YKD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5 M SODIUM FORMATE, PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 34.49000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.60500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.60500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.73500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.60500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.60500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.24500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.60500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.60500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 51.73500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.60500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.60500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 17.24500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 34.49000 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: 1750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 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 HOH A 426 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 MET A 289 REMARK 465 GLU A 290 REMARK 465 HIS A 379 REMARK 465 HIS A 380 REMARK 465 HIS A 381 REMARK 465 HIS A 382 REMARK 465 HIS A 383 REMARK 465 HIS A 384 REMARK 465 MET B 1 REMARK 465 ASN B 20 REMARK 465 ARG B 21 REMARK 465 ARG B 22 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YKC RELATED DB: PDB REMARK 900 RELATED ID: 4YKD RELATED DB: PDB DBREF 4YL6 A 290 376 UNP Q9BSQ5 CCM2_HUMAN 290 376 DBREF 4YL6 B 1 22 UNP Q99759 M3K3_HUMAN 1 22 SEQADV 4YL6 MET A 289 UNP Q9BSQ5 EXPRESSION TAG SEQADV 4YL6 LEU A 377 UNP Q9BSQ5 EXPRESSION TAG SEQADV 4YL6 GLU A 378 UNP Q9BSQ5 EXPRESSION TAG SEQADV 4YL6 HIS A 379 UNP Q9BSQ5 EXPRESSION TAG SEQADV 4YL6 HIS A 380 UNP Q9BSQ5 EXPRESSION TAG SEQADV 4YL6 HIS A 381 UNP Q9BSQ5 EXPRESSION TAG SEQADV 4YL6 HIS A 382 UNP Q9BSQ5 EXPRESSION TAG SEQADV 4YL6 HIS A 383 UNP Q9BSQ5 EXPRESSION TAG SEQADV 4YL6 HIS A 384 UNP Q9BSQ5 EXPRESSION TAG SEQRES 1 A 96 MET GLU LEU SER ALA SER ALA THR GLU LEU LEU GLN ASP SEQRES 2 A 96 TYR MET LEU THR LEU ARG THR LYS LEU SER SER GLN GLU SEQRES 3 A 96 ILE GLN GLN PHE ALA ALA LEU LEU HIS GLU TYR ARG ASN SEQRES 4 A 96 GLY ALA SER ILE HIS GLU PHE CYS ILE ASN LEU ARG GLN SEQRES 5 A 96 LEU TYR GLY ASP SER ARG LYS PHE LEU LEU LEU GLY LEU SEQRES 6 A 96 ARG PRO PHE ILE PRO GLU LYS ASP SER GLN HIS PHE GLU SEQRES 7 A 96 ASN PHE LEU GLU THR ILE GLY VAL LYS ASP LEU GLU HIS SEQRES 8 A 96 HIS HIS HIS HIS HIS SEQRES 1 B 22 MET ASP GLU GLN GLU ALA LEU ASN SER ILE MET ASN ASP SEQRES 2 B 22 LEU VAL ALA LEU GLN MET ASN ARG ARG FORMUL 3 HOH *70(H2 O) HELIX 1 AA1 SER A 292 LEU A 310 1 19 HELIX 2 AA2 SER A 311 ASN A 327 1 17 HELIX 3 AA3 SER A 330 GLY A 343 1 14 HELIX 4 AA4 ARG A 346 GLY A 352 1 7 HELIX 5 AA5 LEU A 353 ILE A 357 5 5 HELIX 6 AA6 PRO A 358 LYS A 360 5 3 HELIX 7 AA7 ASP A 361 GLY A 373 1 13 HELIX 8 AA8 GLU B 3 MET B 19 1 17 CRYST1 61.210 61.210 68.980 90.00 90.00 90.00 P 43 21 2 8 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 0.016337 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016337 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014497 0.00000