HEADER PROTEIN BINDING 14-JAN-11 3QBY TITLE CRYSTAL STRUCTURE OF THE PWWP DOMAIN OF HUMAN HEPATOMA-DERIVED GROWTH TITLE 2 FACTOR 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPATOMA-DERIVED GROWTH FACTOR-RELATED PROTEIN 2; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: UNP RESIDUES 1-93; COMPND 5 SYNONYM: HRP-2, HEPATOMA-DERIVED GROWTH FACTOR 2, HDGF-2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: H4K20ME3 HISTONE H4 PEPTIDE; COMPND 9 CHAIN: H; COMPND 10 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: HDGFRP2, HDGF2, UNQ785/PRO1604; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) V2R-PRARE; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-MHL; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS HDGF2, STRUCTURAL GENOMICS CONSORTIUM, SGC, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR H.ZENG,W.TEMPEL,M.F.AMAYA,M.A.ADAMS-CIOABA,F.MACKENZIE,C.BOUNTRA, AUTHOR 2 J.WEIGELT,C.H.ARROWSMITH,A.M.EDWARDS,J.MIN,H.WU,STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (SGC) REVDAT 5 13-SEP-23 3QBY 1 REMARK SEQADV LINK REVDAT 4 08-NOV-17 3QBY 1 REMARK REVDAT 3 05-SEP-12 3QBY 1 REMARK REVDAT 2 20-JUL-11 3QBY 1 JRNL REVDAT 1 09-FEB-11 3QBY 0 JRNL AUTH H.WU,H.ZENG,R.LAM,W.TEMPEL,M.F.AMAYA,C.XU,L.DOMBROVSKI, JRNL AUTH 2 W.QIU,Y.WANG,J.MIN JRNL TITL STRUCTURAL AND HISTONE BINDING ABILITY CHARACTERIZATIONS OF JRNL TITL 2 HUMAN PWWP DOMAINS. JRNL REF PLOS ONE V. 6 18919 2011 JRNL REFN ESSN 1932-6203 JRNL PMID 21720545 JRNL DOI 10.1371/JOURNAL.PONE.0018919 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 20561 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS (SFTOOLS) REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.131 REMARK 3 FREE R VALUE TEST SET COUNT : 1055 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1480 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.2410 REMARK 3 BIN FREE R VALUE SET COUNT : 0 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2034 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 52 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.07000 REMARK 3 B22 (A**2) : 0.16700 REMARK 3 B33 (A**2) : -1.23700 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.165 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.127 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.598 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2140 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2910 ; 1.210 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 253 ; 7.048 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 99 ;30.319 ;23.535 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 294 ;12.802 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;20.489 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 268 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1713 ; 0.006 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1286 ; 0.611 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2057 ; 1.048 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 854 ; 1.658 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 851 ; 2.547 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -10 A 9999 REMARK 3 ORIGIN FOR THE GROUP (A): 4.3323 -16.2143 -1.8222 REMARK 3 T TENSOR REMARK 3 T11: 0.0109 T22: 0.0903 REMARK 3 T33: 0.0931 T12: -0.0194 REMARK 3 T13: 0.0116 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 5.8772 L22: 2.7555 REMARK 3 L33: 4.4072 L12: -0.3428 REMARK 3 L13: 0.4869 L23: -0.9662 REMARK 3 S TENSOR REMARK 3 S11: -0.0804 S12: 0.0391 S13: -0.2467 REMARK 3 S21: -0.0197 S22: 0.1414 S23: 0.0758 REMARK 3 S31: 0.1556 S32: -0.1178 S33: -0.0610 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B -10 B 9999 REMARK 3 ORIGIN FOR THE GROUP (A): 18.5580 -13.2400 -32.6343 REMARK 3 T TENSOR REMARK 3 T11: 0.2648 T22: 0.0636 REMARK 3 T33: 0.0815 T12: -0.0308 REMARK 3 T13: 0.0970 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 3.3634 L22: 5.7116 REMARK 3 L33: 4.8949 L12: -0.6698 REMARK 3 L13: -1.4167 L23: 0.6001 REMARK 3 S TENSOR REMARK 3 S11: 0.1390 S12: -0.1297 S13: 0.0532 REMARK 3 S21: -0.2282 S22: -0.0094 S23: -0.2424 REMARK 3 S31: 0.0149 S32: 0.1502 S33: -0.1296 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C -10 C 9999 REMARK 3 ORIGIN FOR THE GROUP (A): -1.6451 -34.1639 -19.4962 REMARK 3 T TENSOR REMARK 3 T11: 0.1916 T22: 0.1534 REMARK 3 T33: 0.1731 T12: -0.0490 REMARK 3 T13: 0.0091 T23: 0.0198 REMARK 3 L TENSOR REMARK 3 L11: 6.4375 L22: 6.3775 REMARK 3 L33: 8.0470 L12: 3.5528 REMARK 3 L13: -2.8450 L23: -3.8225 REMARK 3 S TENSOR REMARK 3 S11: -0.1994 S12: 0.2753 S13: 0.1864 REMARK 3 S21: -0.6767 S22: 0.3185 S23: 0.0364 REMARK 3 S31: 0.4840 S32: -0.0654 S33: -0.1191 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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: WITH TLS ADDED. REMARK 4 REMARK 4 3QBY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063451. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97800 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21026 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.18200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PDB ENTRY 3EAE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE, PEPTIDE LIGAND WAS ADDED AT 0.005 M CONCENTRATION, PH REMARK 280 4.6, VAPOR DIFFUSION, TEMPERATURE 291K, VAPOR DIFFUSION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 20.76350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.37450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.84050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 78.37450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.76350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.84050 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, H 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 0 REMARK 465 GLY B 0 REMARK 465 MET B 1 REMARK 465 PRO B 2 REMARK 465 HIS B 3 REMARK 465 ILE B 28 REMARK 465 ALA B 29 REMARK 465 ASP B 30 REMARK 465 GLY B 31 REMARK 465 ALA B 32 REMARK 465 VAL B 33 REMARK 465 LYS B 34 REMARK 465 GLY C 0 REMARK 465 MET C 1 REMARK 465 PRO C 2 REMARK 465 HIS C 3 REMARK 465 ALA C 4 REMARK 465 ASP C 27 REMARK 465 ILE C 28 REMARK 465 ALA C 29 REMARK 465 ASP C 30 REMARK 465 GLY C 31 REMARK 465 ALA C 32 REMARK 465 VAL C 33 REMARK 465 LYS C 34 REMARK 465 PRO C 35 REMARK 465 ALA C 90 REMARK 465 SER C 91 REMARK 465 TYR C 92 REMARK 465 SER C 93 REMARK 465 ALA H 15 REMARK 465 LYS H 16 REMARK 465 ARG H 17 REMARK 465 VAL H 21 REMARK 465 LEU H 22 REMARK 465 ARG H 23 REMARK 465 ASP H 24 REMARK 465 ASN H 25 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 LYS A 16 CD CE NZ REMARK 470 ASP A 27 OD1 OD2 REMARK 470 LYS A 67 CE NZ REMARK 470 LYS A 73 CG CD CE NZ REMARK 470 ARG A 74 NE CZ NH1 NH2 REMARK 470 LYS A 75 CD CE NZ REMARK 470 SER A 93 OG REMARK 470 ASP B 62 CG OD1 OD2 REMARK 470 ASP B 66 CG OD1 OD2 REMARK 470 LYS B 73 CG CD CE NZ REMARK 470 GLU B 79 CD OE1 OE2 REMARK 470 LYS C 6 CG CD CE NZ REMARK 470 LYS C 39 NZ REMARK 470 LYS C 56 CG CD CE NZ REMARK 470 ASP C 62 CG OD1 OD2 REMARK 470 LYS C 63 CD CE NZ REMARK 470 ASP C 66 CG OD1 OD2 REMARK 470 LYS C 67 CE NZ REMARK 470 LYS C 70 CG CD CE NZ REMARK 470 LYS C 73 CE NZ REMARK 470 LYS C 75 CG CD CE NZ REMARK 470 HIS H 18 CG ND1 CD2 CE1 NE2 REMARK 470 ARG H 19 CG CD NE CZ NH1 NH2 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 ASN A 87 64.00 -155.09 REMARK 500 ASN B 87 64.65 -158.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 94 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 95 DBREF 3QBY A 1 93 UNP Q7Z4V5 HDGR2_HUMAN 1 93 DBREF 3QBY B 1 93 UNP Q7Z4V5 HDGR2_HUMAN 1 93 DBREF 3QBY C 1 93 UNP Q7Z4V5 HDGR2_HUMAN 1 93 DBREF 3QBY H 15 25 PDB 3QBY 3QBY 15 25 SEQADV 3QBY GLY A 0 UNP Q7Z4V5 EXPRESSION TAG SEQADV 3QBY GLY B 0 UNP Q7Z4V5 EXPRESSION TAG SEQADV 3QBY GLY C 0 UNP Q7Z4V5 EXPRESSION TAG SEQRES 1 A 94 GLY MET PRO HIS ALA PHE LYS PRO GLY ASP LEU VAL PHE SEQRES 2 A 94 ALA LYS MET LYS GLY TYR PRO HIS TRP PRO ALA ARG ILE SEQRES 3 A 94 ASP ASP ILE ALA ASP GLY ALA VAL LYS PRO PRO PRO ASN SEQRES 4 A 94 LYS TYR PRO ILE PHE PHE PHE GLY THR HIS GLU THR ALA SEQRES 5 A 94 PHE LEU GLY PRO LYS ASP LEU PHE PRO TYR ASP LYS CYS SEQRES 6 A 94 LYS ASP LYS TYR GLY LYS PRO ASN LYS ARG LYS GLY PHE SEQRES 7 A 94 ASN GLU GLY LEU TRP GLU ILE GLN ASN ASN PRO HIS ALA SEQRES 8 A 94 SER TYR SER SEQRES 1 B 94 GLY MET PRO HIS ALA PHE LYS PRO GLY ASP LEU VAL PHE SEQRES 2 B 94 ALA LYS MET LYS GLY TYR PRO HIS TRP PRO ALA ARG ILE SEQRES 3 B 94 ASP ASP ILE ALA ASP GLY ALA VAL LYS PRO PRO PRO ASN SEQRES 4 B 94 LYS TYR PRO ILE PHE PHE PHE GLY THR HIS GLU THR ALA SEQRES 5 B 94 PHE LEU GLY PRO LYS ASP LEU PHE PRO TYR ASP LYS CYS SEQRES 6 B 94 LYS ASP LYS TYR GLY LYS PRO ASN LYS ARG LYS GLY PHE SEQRES 7 B 94 ASN GLU GLY LEU TRP GLU ILE GLN ASN ASN PRO HIS ALA SEQRES 8 B 94 SER TYR SER SEQRES 1 C 94 GLY MET PRO HIS ALA PHE LYS PRO GLY ASP LEU VAL PHE SEQRES 2 C 94 ALA LYS MET LYS GLY TYR PRO HIS TRP PRO ALA ARG ILE SEQRES 3 C 94 ASP ASP ILE ALA ASP GLY ALA VAL LYS PRO PRO PRO ASN SEQRES 4 C 94 LYS TYR PRO ILE PHE PHE PHE GLY THR HIS GLU THR ALA SEQRES 5 C 94 PHE LEU GLY PRO LYS ASP LEU PHE PRO TYR ASP LYS CYS SEQRES 6 C 94 LYS ASP LYS TYR GLY LYS PRO ASN LYS ARG LYS GLY PHE SEQRES 7 C 94 ASN GLU GLY LEU TRP GLU ILE GLN ASN ASN PRO HIS ALA SEQRES 8 C 94 SER TYR SER SEQRES 1 H 11 ALA LYS ARG HIS ARG M3L VAL LEU ARG ASP ASN MODRES 3QBY M3L H 20 LYS N-TRIMETHYLLYSINE HET M3L H 20 12 HET UNX A 94 1 HET UNX A 95 1 HET UNX A 96 1 HET UNX A 97 1 HET UNX A 98 1 HET UNX A 99 1 HET UNX A 100 1 HET UNX A 101 1 HET UNX A 102 1 HET UNX A 103 1 HET UNX A 104 1 HET UNX A 105 1 HET UNX A 106 1 HET SO4 B 94 5 HET SO4 B 95 5 HET UNX B 96 1 HET UNX B 97 1 HET UNX B 98 1 HET UNX B 99 1 HET UNX C 94 1 HET UNX C 95 1 HET UNX C 96 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM UNX UNKNOWN ATOM OR ION HETNAM SO4 SULFATE ION FORMUL 4 M3L C9 H21 N2 O2 1+ FORMUL 5 UNX 20(X) FORMUL 18 SO4 2(O4 S 2-) FORMUL 27 HOH *52(H2 O) HELIX 1 1 GLY A 54 LYS A 56 5 3 HELIX 2 2 TYR A 61 GLY A 69 1 9 HELIX 3 3 GLY A 76 ASN A 87 1 12 HELIX 4 4 GLY B 54 LYS B 56 5 3 HELIX 5 5 TYR B 61 GLY B 69 1 9 HELIX 6 6 GLY B 76 ASN B 87 1 12 HELIX 7 7 GLY C 54 LYS C 56 5 3 HELIX 8 8 TYR C 61 GLY C 69 1 9 HELIX 9 9 GLY C 76 ASN C 87 1 12 SHEET 1 A 5 THR A 50 LEU A 53 0 SHEET 2 A 5 TYR A 40 PHE A 44 -1 N ILE A 42 O ALA A 51 SHEET 3 A 5 TRP A 21 ILE A 25 -1 N ARG A 24 O PHE A 43 SHEET 4 A 5 LEU A 10 ALA A 13 -1 N ALA A 13 O TRP A 21 SHEET 5 A 5 LEU A 58 PRO A 60 -1 O PHE A 59 N PHE A 12 SHEET 1 B 5 THR B 50 LEU B 53 0 SHEET 2 B 5 TYR B 40 PHE B 44 -1 N ILE B 42 O ALA B 51 SHEET 3 B 5 TRP B 21 ILE B 25 -1 N ARG B 24 O PHE B 43 SHEET 4 B 5 LEU B 10 ALA B 13 -1 N ALA B 13 O TRP B 21 SHEET 5 B 5 LEU B 58 PRO B 60 -1 O PHE B 59 N PHE B 12 SHEET 1 C 5 THR C 50 LEU C 53 0 SHEET 2 C 5 TYR C 40 PHE C 44 -1 N TYR C 40 O LEU C 53 SHEET 3 C 5 TRP C 21 ILE C 25 -1 N ARG C 24 O PHE C 43 SHEET 4 C 5 LEU C 10 ALA C 13 -1 N VAL C 11 O ALA C 23 SHEET 5 C 5 LEU C 58 PRO C 60 -1 O PHE C 59 N PHE C 12 LINK C ARG H 19 N M3L H 20 1555 1555 1.33 SITE 1 AC1 6 LYS A 34 LYS B 75 GLY B 76 PHE B 77 SITE 2 AC1 6 ASN B 78 GLU B 79 SITE 1 AC2 3 LYS B 14 LYS B 16 GLY B 17 CRYST1 41.527 41.681 156.749 90.00 90.00 90.00 P 21 21 21 12 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 0.024081 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006380 0.00000