HEADER PEPTIDE BINDING PROTEIN 19-DEC-17 6FBK TITLE CRYSTAL STRUCTURE OF THE HUMAN WNK2 CCT-LIKE 1 DOMAIN IN COMPLEX WITH TITLE 2 A WNK1 RFXV PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE WNK2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ANTIGEN NY-CO-43,PROTEIN KINASE LYSINE-DEFICIENT 2,PROTEIN COMPND 5 KINASE WITH NO LYSINE 2,SEROLOGICALLY DEFINED COLON CANCER ANTIGEN COMPND 6 43; COMPND 7 EC: 2.7.11.1; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: SERINE/THREONINE-PROTEIN KINASE WNK1; COMPND 11 CHAIN: P; COMPND 12 SYNONYM: ERYTHROCYTE 65 KDA PROTEIN,P65,KINASE DEFICIENT PROTEIN, COMPND 13 PROTEIN KINASE LYSINE-DEFICIENT 1,PROTEIN KINASE WITH NO LYSINE 1, COMPND 14 HWNK1; COMPND 15 EC: 2.7.11.1; COMPND 16 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: WNK2, KIAA1760, PRKWNK2, SDCCAG43, P/OKCL.13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS WNK2, CCT DOMAIN, AI DOMAIN, RFXV MOTIF BINDING, PEPTIDE BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.M.PINKAS,J.C.BUFTON,N.A.BURGESS-BROWN,C.H.ARROWSMITH,A.M.EDWARDS, AUTHOR 2 C.BOUNTRA,A.N.BULLOCK REVDAT 2 17-JAN-24 6FBK 1 REMARK REVDAT 1 24-JAN-18 6FBK 0 JRNL AUTH D.M.PINKAS,J.C.BUFTON,N.A.BURGESS-BROWN,C.H.ARROWSMITH, JRNL AUTH 2 A.M.EDWARDS,C.BOUNTRA,A.BULLOCK JRNL TITL CRYSTAL STRUCTURE OF THE HUMAN WNK2 CCT-LIKE 1 DOMAIN IN JRNL TITL 2 COMPLEX WITH A WNK1 RFXV PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 11674 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.287 REMARK 3 R VALUE (WORKING SET) : 0.284 REMARK 3 FREE R VALUE : 0.334 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.720 REMARK 3 FREE R VALUE TEST SET COUNT : 551 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 33.9797 - 2.7663 1.00 2867 137 0.2390 0.2901 REMARK 3 2 2.7663 - 2.1958 1.00 2772 147 0.3765 0.4441 REMARK 3 3 2.1958 - 1.9183 0.97 2706 122 0.3910 0.4551 REMARK 3 4 1.9183 - 1.7429 1.00 2778 145 0.4619 0.4466 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 50.600 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 : 0.008 771 REMARK 3 ANGLE : 0.874 1045 REMARK 3 CHIRALITY : 0.054 124 REMARK 3 PLANARITY : 0.006 135 REMARK 3 DIHEDRAL : 23.092 460 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: REFINEMENT R FACTORS ARE HIGHER THAN REMARK 3 EXPECTED FOR RESOLUTION AND DIFFRACTION IMAGES SHOW DIFFUSE REMARK 3 SPOTS BETWEEN THE INDEXED SPOTS THAT WERE NOT ABLE TO BE REMARK 3 INTEGRATED. NEVERTHELESS, THE STRUCTURE APPEARS CORRECT. REMARK 4 REMARK 4 6FBK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200008045. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11689 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 55.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 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: PHASER REMARK 200 STARTING MODEL: 6ELM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350 -- 10% ETHYLENE GLYCOL -- REMARK 280 0.2M SODIUM FLUORIDE, PH 7.5, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 39.02350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 39.02350 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.86800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.02350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 9.43400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.02350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.30200 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 39.02350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.02350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 18.86800 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 39.02350 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 28.30200 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 39.02350 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 9.43400 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: 1100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P 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 SER A 452 REMARK 465 MET A 453 REMARK 465 ALA A 454 REMARK 465 LYS A 485 REMARK 465 LEU A 486 REMARK 465 LYS A 487 REMARK 465 GLY A 488 REMARK 465 LYS A 489 REMARK 465 PRO A 490 REMARK 465 LYS A 491 REMARK 465 ARG A 545 REMARK 465 ILE A 546 REMARK 465 TRP A 547 REMARK 465 PRO A 548 REMARK 465 ALA A 549 REMARK 465 PRO P 1264 REMARK 465 GLU P 1265 REMARK 465 SER P 1266 REMARK 465 ARG P 1267 REMARK 465 LEU P 1268 REMARK 465 ARG P 1269 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 455 CG CD OE1 OE2 REMARK 470 GLU A 466 CG CD OE1 OE2 REMARK 470 ASP A 467 CG OD1 OD2 REMARK 470 HIS A 468 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 470 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 471 CG CD CE NZ REMARK 470 ASP A 482 CG OD1 OD2 REMARK 470 LYS A 484 CG CD CE NZ REMARK 470 ASP A 492 CG OD1 OD2 REMARK 470 ASN A 493 CG OD1 ND2 REMARK 470 LYS A 530 CG CD CE NZ REMARK 470 ARG A 533 CG CD NE CZ NH1 NH2 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 ARG A 543 O HOH A 601 1.95 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 470 29.05 47.37 REMARK 500 GLU A 516 5.68 -63.34 REMARK 500 REMARK 500 REMARK: NULL DBREF 6FBK A 454 549 UNP Q9Y3S1 WNK2_HUMAN 454 549 DBREF 6FBK P 1247 1269 UNP Q9H4A3 WNK1_HUMAN 1247 1269 SEQADV 6FBK SER A 452 UNP Q9Y3S1 EXPRESSION TAG SEQADV 6FBK MET A 453 UNP Q9Y3S1 EXPRESSION TAG SEQRES 1 A 98 SER MET ALA GLU ASP THR GLY VAL ARG VAL GLU LEU ALA SEQRES 2 A 98 GLU GLU ASP HIS GLY ARG LYS SER THR ILE ALA LEU ARG SEQRES 3 A 98 LEU TRP VAL GLU ASP PRO LYS LYS LEU LYS GLY LYS PRO SEQRES 4 A 98 LYS ASP ASN GLY ALA ILE GLU PHE THR PHE ASP LEU GLU SEQRES 5 A 98 LYS GLU THR PRO ASP GLU VAL ALA GLN GLU MET ILE GLU SEQRES 6 A 98 SER GLY PHE PHE HIS GLU SER ASP VAL LYS ILE VAL ALA SEQRES 7 A 98 LYS SER ILE ARG ASP ARG VAL ALA LEU ILE GLN TRP ARG SEQRES 8 A 98 ARG GLU ARG ILE TRP PRO ALA SEQRES 1 P 23 LEU THR GLN VAL VAL HIS SER ALA GLY ARG ARG PHE ILE SEQRES 2 P 23 VAL SER PRO VAL PRO GLU SER ARG LEU ARG FORMUL 3 HOH *14(H2 O) HELIX 1 AA1 THR A 506 GLU A 516 1 11 HELIX 2 AA2 ASP A 524 ARG A 542 1 19 SHEET 1 AA1 5 VAL A 459 LEU A 463 0 SHEET 2 AA1 5 THR A 473 VAL A 480 -1 O ARG A 477 N GLU A 462 SHEET 3 AA1 5 ALA A 495 ASP A 501 -1 O PHE A 498 N LEU A 476 SHEET 4 AA1 5 ARG P1257 SER P1261 -1 O SER P1261 N ALA A 495 SHEET 5 AA1 5 THR P1248 VAL P1251 -1 N VAL P1250 O PHE P1258 CRYST1 78.047 78.047 37.736 90.00 90.00 90.00 I 41 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 0.012813 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012813 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026500 0.00000