HEADER HYDROLASE 07-SEP-14 4UZQ TITLE STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH O-PALMITOLEOYL TITLE 2 SERINE - CRYSTAL FORM IX - 1.5A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN NOTUM HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 81-451; COMPND 5 SYNONYM: NOTUM; COMPND 6 EC: 3.1.1.1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: GLYCOSYLATED AT N96; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: PROTEIN WNT-7A; COMPND 12 CHAIN: B; COMPND 13 FRAGMENT: RESIDUES 202-209; 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 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293T; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHLSEC; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS HYDROLASE, ESTERASE, EXTRACELLULAR, ALPHA/BETA HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.ZEBISCH,E.Y.JONES REVDAT 4 29-JUL-20 4UZQ 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 18-MAR-15 4UZQ 1 JRNL REVDAT 2 04-MAR-15 4UZQ 1 TITLE REVDAT 1 25-FEB-15 4UZQ 0 JRNL AUTH S.KAKUGAWA,P.F.LANGTON,M.ZEBISCH,S.A.HOWELL,T.CHANG,Y.LIU, JRNL AUTH 2 T.FEIZI,G.BINEVA,N.O'REILLY,A.P.SNIJDERS,E.Y.JONES,J.VINCENT JRNL TITL NOTUM DEACYLATES WNT PROTEINS TO SUPPRESS SIGNALLING JRNL TITL 2 ACTIVITY. JRNL REF NATURE V. 519 187 2015 JRNL REFN ISSN 0028-0836 JRNL PMID 25731175 JRNL DOI 10.1038/NATURE14259 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 62998 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1255 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4294 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.2410 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2849 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 305 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.51000 REMARK 3 B22 (A**2) : 0.67000 REMARK 3 B33 (A**2) : 0.88000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.46000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.061 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.062 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.047 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.980 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3056 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2869 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4163 ; 1.882 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6578 ; 0.944 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 377 ; 6.067 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 150 ;31.774 ;21.933 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 500 ;12.221 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;19.359 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 439 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3462 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 777 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1445 ; 2.828 ; 1.206 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1444 ; 2.812 ; 1.200 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1807 ; 3.194 ; 1.814 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1808 ; 3.205 ; 1.820 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1611 ; 6.608 ; 1.899 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1612 ; 6.606 ; 1.901 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2345 ; 7.582 ; 2.612 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3745 ; 6.321 ;11.939 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3746 ; 6.320 ;11.949 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 5925 ; 4.387 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 134 ;38.727 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6008 ;18.012 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4UZQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1290061715. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 4 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) : 1.00,1.07 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64352 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6000 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: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.0M NACL, 0.1 M CITRATE PH 5.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 22.85028 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.67500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.43562 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 22.85028 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.67500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 60.43562 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -90.6 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 50.51300 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 A2146 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 GLU A 78 REMARK 465 THR A 79 REMARK 465 GLY A 80 REMARK 465 SER A 81 REMARK 465 ALA A 82 REMARK 465 GLN A 83 REMARK 465 GLN A 84 REMARK 465 LEU A 85 REMARK 465 ASN A 86 REMARK 465 ASP A 420 REMARK 465 SER A 421 REMARK 465 HIS A 422 REMARK 465 LYS A 423 REMARK 465 ALA A 424 REMARK 465 SER A 425 REMARK 465 LYS A 426 REMARK 465 THR A 427 REMARK 465 PRO A 428 REMARK 465 LEU A 429 REMARK 465 GLY A 452 REMARK 465 THR A 453 REMARK 465 HIS A 454 REMARK 465 HIS A 455 REMARK 465 HIS A 456 REMARK 465 HIS A 457 REMARK 465 HIS A 458 REMARK 465 HIS A 459 REMARK 465 HIS A 460 REMARK 465 HIS A 461 REMARK 465 HIS A 462 REMARK 465 HIS A 463 REMARK 465 CYS B 202 REMARK 465 HIS B 203 REMARK 465 GLY B 204 REMARK 465 VAL B 205 REMARK 465 GLY B 275 REMARK 465 SER B 208 REMARK 465 CYS B 209 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 168 CD GLU A 168 OE1 0.075 REMARK 500 GLU A 168 CD GLU A 168 OE2 0.068 REMARK 500 GLU A 214 CD GLU A 214 OE2 0.087 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 139 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 139 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 144 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 144 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 213 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG A 213 NE - CZ - NH1 ANGL. DEV. = 10.0 DEGREES REMARK 500 ARG A 213 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 218 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 218 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 275 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ASP A 278 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 307 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 416 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES 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 TRP A 128 -142.62 53.50 REMARK 500 ALA A 232 -120.65 63.28 REMARK 500 PHE A 339 73.91 -118.10 REMARK 500 GLU A 390 155.08 69.50 REMARK 500 ILE A 391 -41.24 -153.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 GAMMA-PALMITOLEOYL-SERINE: WNT FRAGMENT ESTER BETWEEN REMARK 600 SERINE OF WNT FRAGMENT AND PALMITOLEIC ACID 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 NA A1456 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 103 O REMARK 620 2 SER A 439 OG 164.4 REMARK 620 3 HOH A2054 O 87.8 80.4 REMARK 620 4 HOH A2058 O 82.3 86.2 83.0 REMARK 620 5 HOH A2222 O 95.9 94.7 92.9 175.6 REMARK 620 6 HOH A2235 O 101.9 88.7 167.7 90.7 93.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1455 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 283 O REMARK 620 2 THR A 345 O 102.8 REMARK 620 3 ASN A 348 OD1 119.2 97.6 REMARK 620 4 HOH A2149 O 90.1 166.3 71.8 REMARK 620 5 HOH A2230 O 126.6 94.5 107.6 81.0 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UYU RELATED DB: PDB REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM I IODIDE REMARK 900 COMPLEX - 2.3A REMARK 900 RELATED ID: 4UYW RELATED DB: PDB REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM I HEPARIN REMARK 900 FRAGMENT COMPLEX - 1.7A REMARK 900 RELATED ID: 4UYZ RELATED DB: PDB REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM II - 2.8A REMARK 900 RELATED ID: 4UZ1 RELATED DB: PDB REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM III - 1.4A REMARK 900 RELATED ID: 4UZ5 RELATED DB: PDB REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM IV - 2.1A REMARK 900 RELATED ID: 4UZ6 RELATED DB: PDB REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM V - SOS COMPLEX REMARK 900 - 1.9A REMARK 900 RELATED ID: 4UZ7 RELATED DB: PDB REMARK 900 STRUCTURE OF THE WNT DEACETYLASE NOTUM - CRYSTAL FORM VII - SOS REMARK 900 COMPLEX - 2.2A REMARK 900 RELATED ID: 4UZ9 RELATED DB: PDB REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM VII - SOS REMARK 900 COMPLEX - 2.2A REMARK 900 RELATED ID: 4UZA RELATED DB: PDB REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM VIII - REMARK 900 PHOSPHATE COMPLEX - 2.4A REMARK 900 RELATED ID: 4UZJ RELATED DB: PDB REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM III - 1.4A REMARK 900 RELATED ID: 4UZK RELATED DB: PDB REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM FROM DROSOPHILA - CRYSTAL FORM REMARK 900 II - 1.9A REMARK 900 RELATED ID: 4UZL RELATED DB: PDB REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM I MYRISTOLEATE REMARK 900 COMPLEX - 2.1A REMARK 900 RELATED ID: 4WBH RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 C330S ENGINEERED MUTATION S232A INACTIVE MUTANT DBREF 4UZQ A 81 451 UNP Q6P988 NOTUM_HUMAN 81 451 DBREF 4UZQ B 202 209 UNP O00755 WNT7A_HUMAN 202 209 SEQADV 4UZQ GLU A 78 UNP Q6P988 EXPRESSION TAG SEQADV 4UZQ THR A 79 UNP Q6P988 EXPRESSION TAG SEQADV 4UZQ GLY A 80 UNP Q6P988 EXPRESSION TAG SEQADV 4UZQ GLY A 452 UNP Q6P988 EXPRESSION TAG SEQADV 4UZQ THR A 453 UNP Q6P988 EXPRESSION TAG SEQADV 4UZQ HIS A 454 UNP Q6P988 EXPRESSION TAG SEQADV 4UZQ HIS A 455 UNP Q6P988 EXPRESSION TAG SEQADV 4UZQ HIS A 456 UNP Q6P988 EXPRESSION TAG SEQADV 4UZQ HIS A 457 UNP Q6P988 EXPRESSION TAG SEQADV 4UZQ HIS A 458 UNP Q6P988 EXPRESSION TAG SEQADV 4UZQ HIS A 459 UNP Q6P988 EXPRESSION TAG SEQADV 4UZQ HIS A 460 UNP Q6P988 EXPRESSION TAG SEQADV 4UZQ HIS A 461 UNP Q6P988 EXPRESSION TAG SEQADV 4UZQ HIS A 462 UNP Q6P988 EXPRESSION TAG SEQADV 4UZQ HIS A 463 UNP Q6P988 EXPRESSION TAG SEQADV 4UZQ ALA A 232 UNP Q6P988 SER 232 ENGINEERED MUTATION SEQADV 4UZQ SER A 330 UNP Q6P988 CYS 330 ENGINEERED MUTATION SEQRES 1 A 386 GLU THR GLY SER ALA GLN GLN LEU ASN GLU ASP LEU ARG SEQRES 2 A 386 LEU HIS LEU LEU LEU ASN THR SER VAL THR CYS ASN ASP SEQRES 3 A 386 GLY SER PRO ALA GLY TYR TYR LEU LYS GLU SER ARG GLY SEQRES 4 A 386 SER ARG ARG TRP LEU LEU PHE LEU GLU GLY GLY TRP TYR SEQRES 5 A 386 CYS PHE ASN ARG GLU ASN CYS ASP SER ARG TYR ASP THR SEQRES 6 A 386 MET ARG ARG LEU MET SER SER ARG ASP TRP PRO ARG THR SEQRES 7 A 386 ARG THR GLY THR GLY ILE LEU SER SER GLN PRO GLU GLU SEQRES 8 A 386 ASN PRO TYR TRP TRP ASN ALA ASN MET VAL PHE ILE PRO SEQRES 9 A 386 TYR CYS SER SER ASP VAL TRP SER GLY ALA SER SER LYS SEQRES 10 A 386 SER GLU LYS ASN GLU TYR ALA PHE MET GLY ALA LEU ILE SEQRES 11 A 386 ILE GLN GLU VAL VAL ARG GLU LEU LEU GLY ARG GLY LEU SEQRES 12 A 386 SER GLY ALA LYS VAL LEU LEU LEU ALA GLY SER ALA ALA SEQRES 13 A 386 GLY GLY THR GLY VAL LEU LEU ASN VAL ASP ARG VAL ALA SEQRES 14 A 386 GLU GLN LEU GLU LYS LEU GLY TYR PRO ALA ILE GLN VAL SEQRES 15 A 386 ARG GLY LEU ALA ASP SER GLY TRP PHE LEU ASP ASN LYS SEQRES 16 A 386 GLN TYR ARG HIS THR ASP CYS VAL ASP THR ILE THR CYS SEQRES 17 A 386 ALA PRO THR GLU ALA ILE ARG ARG GLY ILE ARG TYR TRP SEQRES 18 A 386 ASN GLY VAL VAL PRO GLU ARG CYS ARG ARG GLN PHE GLN SEQRES 19 A 386 GLU GLY GLU GLU TRP ASN CYS PHE PHE GLY TYR LYS VAL SEQRES 20 A 386 TYR PRO THR LEU ARG SER PRO VAL PHE VAL VAL GLN TRP SEQRES 21 A 386 LEU PHE ASP GLU ALA GLN LEU THR VAL ASP ASN VAL HIS SEQRES 22 A 386 LEU THR GLY GLN PRO VAL GLN GLU GLY LEU ARG LEU TYR SEQRES 23 A 386 ILE GLN ASN LEU GLY ARG GLU LEU ARG HIS THR LEU LYS SEQRES 24 A 386 ASP VAL PRO ALA SER PHE ALA PRO ALA CYS LEU SER HIS SEQRES 25 A 386 GLU ILE ILE ILE ARG SER HIS TRP THR ASP VAL GLN VAL SEQRES 26 A 386 LYS GLY THR SER LEU PRO ARG ALA LEU HIS CYS TRP ASP SEQRES 27 A 386 ARG SER LEU HIS ASP SER HIS LYS ALA SER LYS THR PRO SEQRES 28 A 386 LEU LYS GLY CYS PRO VAL HIS LEU VAL ASP SER CYS PRO SEQRES 29 A 386 TRP PRO HIS CYS ASN PRO SER CYS PRO THR GLY THR HIS SEQRES 30 A 386 HIS HIS HIS HIS HIS HIS HIS HIS HIS SEQRES 1 B 8 CYS HIS GLY VAL SER GLY SER CYS MODRES 4UZQ ASN A 96 ASN GLYCOSYLATION SITE HET NAG A1452 14 HET NA A1455 1 HET NA A1456 1 HET CL A1457 1 HET CL A1458 1 HET CL A1459 1 HET PAM B1206 17 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM PAM PALMITOLEIC ACID FORMUL 3 NAG C8 H15 N O6 FORMUL 4 NA 2(NA 1+) FORMUL 6 CL 3(CL 1-) FORMUL 9 PAM C16 H30 O2 FORMUL 10 HOH *305(H2 O) HELIX 1 1 ASN A 132 MET A 143 1 12 HELIX 2 2 ARG A 144 MET A 147 5 4 HELIX 3 3 THR A 159 SER A 163 5 5 HELIX 4 4 MET A 203 GLY A 217 1 15 HELIX 5 5 ARG A 218 ALA A 223 5 6 HELIX 6 6 ALA A 232 LEU A 252 1 21 HELIX 7 7 ALA A 286 ASN A 299 1 14 HELIX 8 8 PRO A 303 ARG A 308 1 6 HELIX 9 9 GLU A 314 PHE A 319 5 6 HELIX 10 10 PHE A 320 TYR A 325 1 6 HELIX 11 11 PRO A 326 LEU A 328 5 3 HELIX 12 12 GLU A 341 ASP A 347 1 7 HELIX 13 13 GLN A 357 LYS A 376 1 20 HELIX 14 14 LEU A 407 HIS A 419 1 13 SHEET 1 AA10 THR A 155 ARG A 156 0 SHEET 2 AA10 LEU A 89 LEU A 93 -1 O LEU A 89 N ARG A 156 SHEET 3 AA10 GLY A 108 LYS A 112 -1 O TYR A 109 N HIS A 92 SHEET 4 AA10 ASN A 176 ILE A 180 -1 O MET A 177 N LYS A 112 SHEET 5 AA10 ARG A 119 LEU A 124 1 O ARG A 119 N ASN A 176 SHEET 6 AA10 VAL A 225 SER A 231 1 O VAL A 225 N TRP A 120 SHEET 7 AA10 GLN A 258 ASP A 264 1 O GLN A 258 N LEU A 226 SHEET 8 AA10 VAL A 332 VAL A 335 1 O PHE A 333 N ALA A 263 SHEET 9 AA10 SER A 381 ALA A 383 1 N PHE A 382 O VAL A 334 SHEET 10 AA10 HIS A 435 VAL A 437 1 O LEU A 436 N ALA A 383 SHEET 1 AB 2 PHE A 339 ASP A 340 0 SHEET 2 AB 2 LEU A 387 SER A 388 1 N SER A 388 O PHE A 339 SHEET 1 AC 2 GLN A 401 VAL A 402 0 SHEET 2 AC 2 THR A 405 SER A 406 -1 O THR A 405 N VAL A 402 SSBOND 1 CYS A 101 CYS A 183 1555 1555 2.12 SSBOND 2 CYS A 130 CYS A 136 1555 1555 1.97 SSBOND 3 CYS A 279 CYS A 285 1555 1555 2.07 SSBOND 4 CYS A 306 CYS A 318 1555 1555 2.15 SSBOND 5 CYS A 386 CYS A 449 1555 1555 2.01 SSBOND 6 CYS A 413 CYS A 432 1555 1555 2.01 SSBOND 7 CYS A 440 CYS A 445 1555 1555 2.06 LINK ND2 ASN A 96 C1 NAG A1452 1555 1555 1.47 LINK OG SER B 206 C1 PAM B1206 1555 1555 1.34 LINK O ASP A 103 NA NA A1456 1655 1555 2.74 LINK O ILE A 283 NA NA A1455 1555 1555 2.23 LINK O THR A 345 NA NA A1455 1555 1555 2.31 LINK OD1 ASN A 348 NA NA A1455 1555 1555 2.22 LINK OG SER A 439 NA NA A1456 1555 1555 2.43 LINK NA NA A1455 O HOH A2149 1555 4555 2.72 LINK NA NA A1455 O HOH A2230 1555 1555 2.35 LINK NA NA A1456 O HOH A2054 1555 1555 2.41 LINK NA NA A1456 O HOH A2058 1555 1555 2.47 LINK NA NA A1456 O HOH A2222 1555 1555 2.48 LINK NA NA A1456 O HOH A2235 1555 1555 2.41 CRYST1 50.513 69.350 120.967 90.00 92.28 90.00 I 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 0.019797 0.000000 0.000788 0.00000 SCALE2 0.000000 0.014420 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008273 0.00000