PDB Short entry for 2VPG HEADER GENE REGULATION 27-FEB-08 2VPG TITLE DECODING OF METHYLATED HISTONE H3 TAIL BY THE PYGO-BCL9 WNT SIGNALING TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYGOPUS HOMOLOG 1; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: PHD DOMAIN, RESIDUES 340-398; COMPND 5 SYNONYM: HPYGO1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: B-CELL CLL/LYMPHOMA 9 PROTEIN; COMPND 9 CHAIN: B, D; COMPND 10 FRAGMENT: HD1 DOMAIN, RESIDUES 177-205; COMPND 11 SYNONYM: B-CELL LYMPHOMA 9 PROTEIN, BCL-9, PROTEIN LEGLESS HOMOLOG, COMPND 12 BCL9; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: HISTONE H3 TAIL; COMPND 16 CHAIN: P, R; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: 18-MER H3R2ME2AK4ME2, DIMETHYLATION AT LYS K4, COMPND 19 ASYMMETRIC DIMETHYLATION AT R2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: CODONPLUS-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: BI-CISTRONIC EXPRESSION VECTOR; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_VARIANT: CODONPLUS-RIL; SOURCE 18 EXPRESSION_SYSTEM_VECTOR: BI-CISTRONIC EXPRESSION VECTOR; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 22 ORGANISM_COMMON: HUMAN; SOURCE 23 ORGANISM_TAXID: 9606 KEYWDS GENE REGULATION, WNT SIGNALING PATHWAY, WNT SIGNALING COMPLEX, KEYWDS 2 CHROMOSOMAL REARRANGEMENT, SIGNALING PROTEIN, BCL9 HD1 DOMAIN, KEYWDS 3 HPYGO1 PHD DOMAIN, PROTO-ONCOGENE, PHOSPHOPROTEIN, HISTONE H3K4ME2, KEYWDS 4 ZINC, NUCLEUS, ZINC-FINGER, METAL-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.FIEDLER,M.J.SANCHEZ-BARRENA,M.NEKRASOV,J.MIESZCZANEK,V.RYBIN, AUTHOR 2 J.MULLER,M.BIENZ,P.EVANS REVDAT 7 13-DEC-23 2VPG 1 REMARK LINK REVDAT 6 29-MAY-19 2VPG 1 REMARK REVDAT 5 08-MAY-19 2VPG 1 REMARK SEQRES LINK REVDAT 4 06-NOV-13 2VPG 1 SOURCE REMARK VERSN HETNAM REVDAT 4 2 1 HETSYN FORMUL HETATM REVDAT 3 24-FEB-09 2VPG 1 VERSN REVDAT 2 30-SEP-08 2VPG 1 JRNL REVDAT 1 17-JUN-08 2VPG 0 JRNL AUTH M.FIEDLER,M.J.SANCHEZ-BARRENA,M.NEKRASOV,J.MIESZCZANEK, JRNL AUTH 2 V.RYBIN,J.MULLER,P.EVANS,M.BIENZ JRNL TITL DECODING OF METHYLATED HISTONE H3 TAIL BY THE PYGO- BCL9 WNT JRNL TITL 2 SIGNALING COMPLEX. JRNL REF MOL.CELL V. 30 507 2008 JRNL REFN ISSN 1097-2765 JRNL PMID 18498752 JRNL DOI 10.1016/J.MOLCEL.2008.03.011 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0037 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 74.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 37079 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1953 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2732 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 113 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1477 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 259 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.65000 REMARK 3 B22 (A**2) : 0.65000 REMARK 3 B33 (A**2) : -1.29000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.079 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.706 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1514 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2047 ; 1.210 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 194 ; 5.357 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 58 ;31.323 ;26.207 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 228 ;11.379 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ;14.252 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 240 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1109 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 720 ; 0.192 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1049 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 166 ; 0.137 ; 0.200 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): 91 ; 0.181 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 25 ; 0.119 ; 0.200 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): 1003 ; 0.822 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1557 ; 1.406 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 593 ; 2.040 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 490 ; 3.125 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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. REMARK 4 REMARK 4 2VPG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1290035478. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-07 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 : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : DIAMOND (111), GE(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37079 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 26.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.60000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 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: PDB ENTRY 2VPE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING-DROP VAPOUR-DIFFUSION METHOD REMARK 280 AT 19 CELSIUS. CRYSTALLIZATION CONDITIONS: 20% PEG-4000, 20% ISO- REMARK 280 PROPANOL, 0.1 M NA CITRATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 2 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 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 52.87500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.87500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.87500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.87500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.87500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.87500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.87500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.87500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, R 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 336 REMARK 465 ALA A 337 REMARK 465 HIS B 204 REMARK 465 ILE B 205 REMARK 465 HIS D 204 REMARK 465 ILE D 205 REMARK 465 ARG P 8 REMARK 465 LYS P 9 REMARK 465 SER P 10 REMARK 465 THR P 11 REMARK 465 GLY P 12 REMARK 465 GLY P 13 REMARK 465 LYS P 14 REMARK 465 ALA P 15 REMARK 465 PRO P 16 REMARK 465 ARG P 17 REMARK 465 LYS P 18 REMARK 465 ARG R 8 REMARK 465 LYS R 9 REMARK 465 SER R 10 REMARK 465 THR R 11 REMARK 465 GLY R 12 REMARK 465 GLY R 13 REMARK 465 LYS R 14 REMARK 465 ALA R 15 REMARK 465 PRO R 16 REMARK 465 ARG R 17 REMARK 465 LYS R 18 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 THR A 347 -4.47 71.21 REMARK 500 SER A 362 -70.98 -152.11 REMARK 500 ILE C 345 -63.17 -101.42 REMARK 500 THR C 347 -2.83 70.97 REMARK 500 SER C 362 -67.13 -155.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH D2010 DISTANCE = 5.83 ANGSTROMS 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 A1400 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 343 SG REMARK 620 2 CYS A 346 SG 109.8 REMARK 620 3 HIS A 368 ND1 99.7 101.0 REMARK 620 4 CYS A 371 SG 117.2 110.0 117.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 359 SG REMARK 620 2 CYS A 363 SG 109.8 REMARK 620 3 CYS A 392 SG 116.6 114.8 REMARK 620 4 CYS A 395 SG 110.2 105.0 99.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C1399 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 343 SG REMARK 620 2 CYS C 346 SG 109.8 REMARK 620 3 HIS C 368 ND1 99.8 101.2 REMARK 620 4 CYS C 371 SG 116.8 111.3 116.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C1400 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 359 SG REMARK 620 2 CYS C 363 SG 108.3 REMARK 620 3 CYS C 392 SG 116.3 114.3 REMARK 620 4 CYS C 395 SG 113.0 107.7 96.7 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 GOL A 1399 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 1399 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 1400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VP7 RELATED DB: PDB REMARK 900 DECODING OF METHYLATED HISTONE H3 TAIL BY THE PYGO-BCL9 WNT REMARK 900 SIGNALING COMPLEX REMARK 900 RELATED ID: 2VPB RELATED DB: PDB REMARK 900 DECODING OF METHYLATED HISTONE H3 TAIL BY THE PYGO-BCL9 WNT REMARK 900 SIGNALING COMPLEX REMARK 900 RELATED ID: 2VPD RELATED DB: PDB REMARK 900 DECODING OF METHYLATED HISTONE H3 TAIL BY THE PYGO-BCL9 WNT REMARK 900 SIGNALING COMPLEX REMARK 900 RELATED ID: 2VPE RELATED DB: PDB REMARK 900 DECODING OF METHYLATED HISTONE H3 TAIL BY THE PYGO-BCL9 WNT REMARK 900 SIGNALING COMPLEX DBREF 2VPG A 336 339 PDB 2VPG 2VPG 336 339 DBREF 2VPG A 340 398 UNP Q9Y3Y4 PYGO1_HUMAN 340 398 DBREF 2VPG B 174 176 PDB 2VPG 2VPG 174 176 DBREF 2VPG B 177 205 UNP O00512 BCL9_HUMAN 177 205 DBREF 2VPG C 336 339 PDB 2VPG 2VPG 336 339 DBREF 2VPG C 340 398 UNP Q9Y3Y4 PYGO1_HUMAN 340 398 DBREF 2VPG D 174 176 PDB 2VPG 2VPG 174 176 DBREF 2VPG D 177 205 UNP O00512 BCL9_HUMAN 177 205 DBREF 2VPG P 1 18 PDB 2VPG 2VPG 1 18 DBREF 2VPG R 1 18 PDB 2VPG 2VPG 1 18 SEQRES 1 A 63 GLY ALA MET ALA VAL TYR PRO CYS GLY ILE CYS THR ASN SEQRES 2 A 63 GLU VAL ASN ASP ASP GLN ASP ALA ILE LEU CYS GLU ALA SEQRES 3 A 63 SER CYS GLN LYS TRP PHE HIS ARG ILE CYS THR GLY MET SEQRES 4 A 63 THR GLU THR ALA TYR GLY LEU LEU THR ALA GLU ALA SER SEQRES 5 A 63 ALA VAL TRP GLY CYS ASP THR CYS MET ALA ASP SEQRES 1 B 32 GLY ALA MET VAL TYR VAL PHE SER THR GLU MET ALA ASN SEQRES 2 B 32 LYS ALA ALA GLU ALA VAL LEU LYS GLY GLN VAL GLU THR SEQRES 3 B 32 ILE VAL SER PHE HIS ILE SEQRES 1 C 63 GLY ALA MET ALA VAL TYR PRO CYS GLY ILE CYS THR ASN SEQRES 2 C 63 GLU VAL ASN ASP ASP GLN ASP ALA ILE LEU CYS GLU ALA SEQRES 3 C 63 SER CYS GLN LYS TRP PHE HIS ARG ILE CYS THR GLY MET SEQRES 4 C 63 THR GLU THR ALA TYR GLY LEU LEU THR ALA GLU ALA SER SEQRES 5 C 63 ALA VAL TRP GLY CYS ASP THR CYS MET ALA ASP SEQRES 1 D 32 GLY ALA MET VAL TYR VAL PHE SER THR GLU MET ALA ASN SEQRES 2 D 32 LYS ALA ALA GLU ALA VAL LEU LYS GLY GLN VAL GLU THR SEQRES 3 D 32 ILE VAL SER PHE HIS ILE SEQRES 1 P 18 ALA DA2 THR MLY GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 P 18 LYS ALA PRO ARG LYS SEQRES 1 R 18 ALA DA2 THR MLY GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 R 18 LYS ALA PRO ARG LYS MODRES 2VPG DA2 P 2 ARG NG,NG-DIMETHYL-L-ARGININE MODRES 2VPG MLY P 4 LYS N-DIMETHYL-LYSINE MODRES 2VPG DA2 R 2 ARG NG,NG-DIMETHYL-L-ARGININE MODRES 2VPG MLY R 4 LYS N-DIMETHYL-LYSINE HET DA2 P 2 13 HET MLY P 4 11 HET DA2 R 2 26 HET MLY R 4 11 HET GOL A1399 6 HET ZN A1400 1 HET ZN A1401 1 HET ZN C1399 1 HET ZN C1400 1 HETNAM DA2 NG,NG-DIMETHYL-L-ARGININE HETNAM MLY N-DIMETHYL-LYSINE HETNAM GOL GLYCEROL HETNAM ZN ZINC ION HETSYN DA2 ADMA HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 DA2 2(C8 H18 N4 O2) FORMUL 5 MLY 2(C8 H18 N2 O2) FORMUL 7 GOL C3 H8 O3 FORMUL 8 ZN 4(ZN 2+) FORMUL 12 HOH *259(H2 O) HELIX 1 1 ARG A 369 GLY A 373 1 5 HELIX 2 2 THR A 375 GLU A 385 1 11 HELIX 3 3 CYS A 392 ASP A 398 1 7 HELIX 4 4 SER B 181 LYS B 194 1 14 HELIX 5 5 ARG C 369 GLY C 373 1 5 HELIX 6 6 THR C 375 GLU C 385 1 11 HELIX 7 7 CYS C 392 ASP C 398 1 7 HELIX 8 8 SER D 181 LYS D 194 1 14 SHEET 1 AA 2 ALA A 356 LEU A 358 0 SHEET 2 AA 2 TRP A 366 HIS A 368 -1 O PHE A 367 N ILE A 357 SHEET 1 AB 2 ALA A 388 TRP A 390 0 SHEET 2 AB 2 TYR B 178 PHE B 180 1 O TYR B 178 N VAL A 389 SHEET 1 CA 2 ALA C 356 LEU C 358 0 SHEET 2 CA 2 TRP C 366 HIS C 368 -1 O PHE C 367 N ILE C 357 SHEET 1 CB 2 ALA C 388 TRP C 390 0 SHEET 2 CB 2 TYR D 178 PHE D 180 1 O TYR D 178 N VAL C 389 LINK C ALA P 1 N DA2 P 2 1555 1555 1.33 LINK C DA2 P 2 N THR P 3 1555 1555 1.33 LINK C THR P 3 N MLY P 4 1555 1555 1.33 LINK C MLY P 4 N GLN P 5 1555 1555 1.33 LINK C ALA R 1 N BDA2 R 2 1555 1555 1.33 LINK C ALA R 1 N ADA2 R 2 1555 1555 1.33 LINK C ADA2 R 2 N THR R 3 1555 1555 1.33 LINK C BDA2 R 2 N THR R 3 1555 1555 1.33 LINK C THR R 3 N MLY R 4 1555 1555 1.33 LINK C MLY R 4 N GLN R 5 1555 1555 1.33 LINK SG CYS A 343 ZN ZN A1400 1555 1555 2.33 LINK SG CYS A 346 ZN ZN A1400 1555 1555 2.32 LINK SG CYS A 359 ZN ZN A1401 1555 1555 2.22 LINK SG CYS A 363 ZN ZN A1401 1555 1555 2.35 LINK ND1 HIS A 368 ZN ZN A1400 1555 1555 2.08 LINK SG CYS A 371 ZN ZN A1400 1555 1555 2.31 LINK SG CYS A 392 ZN ZN A1401 1555 1555 2.40 LINK SG CYS A 395 ZN ZN A1401 1555 1555 2.37 LINK SG CYS C 343 ZN ZN C1399 1555 1555 2.38 LINK SG CYS C 346 ZN ZN C1399 1555 1555 2.33 LINK SG CYS C 359 ZN ZN C1400 1555 1555 2.25 LINK SG CYS C 363 ZN ZN C1400 1555 1555 2.32 LINK ND1 HIS C 368 ZN ZN C1399 1555 1555 2.15 LINK SG CYS C 371 ZN ZN C1399 1555 1555 2.32 LINK SG CYS C 392 ZN ZN C1400 1555 1555 2.46 LINK SG CYS C 395 ZN ZN C1400 1555 1555 2.40 SITE 1 AC1 6 GLN A 354 HIS A 368 HOH A2092 HOH A2093 SITE 2 AC1 6 GLY C 336 ASN C 348 SITE 1 AC2 4 CYS C 343 CYS C 346 HIS C 368 CYS C 371 SITE 1 AC3 4 CYS C 359 CYS C 363 CYS C 392 CYS C 395 SITE 1 AC4 4 CYS A 343 CYS A 346 HIS A 368 CYS A 371 SITE 1 AC5 4 CYS A 359 CYS A 363 CYS A 392 CYS A 395 CRYST1 105.750 105.750 51.420 90.00 90.00 90.00 P 4 21 2 16 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 0.009456 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009456 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019448 0.00000