HEADER PROTEIN BINDING 11-MAR-21 7M10 TITLE PHF2 PHD DOMAIN COMPLEXED WITH PEPTIDE FROM N-TERMINUS OF VRK1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE PHF2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHD DOMAIN; COMPND 5 SYNONYM: GRC5,PHD FINGER PROTEIN 2; COMPND 6 EC: 1.14.11.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SERINE/THREONINE-PROTEIN KINASE VRK1 N-TERMINUS PEPTIDE; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: VACCINIA-RELATED KINASE 1; COMPND 12 EC: 2.7.11.1; 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: PHF2, CENP-35, KIAA0662; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: GOLD PLUS; 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 PHD FINGER, METAL-BINDING, ZINC-FINGER, HISTONE-BINDING, NON-HISTONE KEYWDS 2 BINDING, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HORTON,X.CHENG REVDAT 3 18-OCT-23 7M10 1 REMARK REVDAT 2 09-JUN-21 7M10 1 JRNL REVDAT 1 26-MAY-21 7M10 0 JRNL AUTH J.CHEN,J.HORTON,C.SAGUM,J.ZHOU,X.CHENG,M.T.BEDFORD JRNL TITL HISTONE H3 N-TERMINAL MIMICRY DRIVES A NOVEL NETWORK OF JRNL TITL 2 METHYL-EFFECTOR INTERACTIONS. JRNL REF BIOCHEM.J. V. 478 1943 2021 JRNL REFN ESSN 1470-8728 JRNL PMID 33969871 JRNL DOI 10.1042/BCJ20210203 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.4 REMARK 3 NUMBER OF REFLECTIONS : 33196 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1668 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 2.6300 - 2.0900 1.00 3287 167 0.1559 0.1615 REMARK 3 2 2.0900 - 1.8200 0.98 3174 167 0.1403 0.1445 REMARK 3 3 1.8200 - 1.6600 0.99 3190 167 0.1357 0.1495 REMARK 3 4 1.6600 - 1.5400 0.99 3184 166 0.1358 0.1677 REMARK 3 5 1.5400 - 1.4500 0.98 3127 167 0.1382 0.1740 REMARK 3 6 1.4500 - 1.3700 0.94 2995 167 0.1542 0.1695 REMARK 3 7 1.3700 - 1.3100 0.86 2707 167 0.1659 0.2095 REMARK 3 8 1.3100 - 1.2600 0.76 2378 166 0.2235 0.2610 REMARK 3 9 1.2200 - 1.1800 0.41 1193 167 0.2597 0.2962 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.107 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.855 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.83 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.61 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 : 0.004 681 REMARK 3 ANGLE : 0.785 921 REMARK 3 CHIRALITY : 0.082 94 REMARK 3 PLANARITY : 0.006 117 REMARK 3 DIHEDRAL : 10.806 251 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 7M10 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000255448. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33230 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 32.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 81.5 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 24.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.57900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3KQI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5M SODIUM FORMATE,100MM TRIS PH 8.2, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 17.12000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.85850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.57600 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 17.12000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.85850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.57600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 17.12000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 31.85850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.57600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 17.12000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 31.85850 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.57600 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 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 227 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 292 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 307 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 GLY A -3 REMARK 465 SER A -2 REMARK 465 ILE A -1 REMARK 465 ASN A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLY B 9 REMARK 465 ARG B 10 REMARK 465 GLN B 11 REMARK 465 SER B 12 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 CYS A 8 175.57 75.27 REMARK 500 REMARK 500 REMARK: NULL 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 A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 8 SG REMARK 620 2 CYS A 10 SG 114.1 REMARK 620 3 HIS A 31 ND1 103.8 96.3 REMARK 620 4 CYS A 34 SG 109.0 120.4 111.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 23 SG REMARK 620 2 CYS A 26 SG 104.3 REMARK 620 3 CYS A 50 SG 112.1 117.9 REMARK 620 4 CYS A 53 SG 109.0 109.6 103.9 REMARK 620 N 1 2 3 DBREF 7M10 A 1 70 UNP O75151 PHF2_HUMAN 1 70 DBREF 7M10 B 1 12 UNP Q99986 VRK1_HUMAN 2 13 SEQADV 7M10 GLY A -3 UNP O75151 EXPRESSION TAG SEQADV 7M10 SER A -2 UNP O75151 EXPRESSION TAG SEQADV 7M10 ILE A -1 UNP O75151 EXPRESSION TAG SEQADV 7M10 ASN A 0 UNP O75151 EXPRESSION TAG SEQRES 1 A 74 GLY SER ILE ASN MET ALA THR VAL PRO VAL TYR CYS VAL SEQRES 2 A 74 CYS ARG LEU PRO TYR ASP VAL THR ARG PHE MET ILE GLU SEQRES 3 A 74 CYS ASP ALA CYS LYS ASP TRP PHE HIS GLY SER CYS VAL SEQRES 4 A 74 GLY VAL GLU GLU GLU GLU ALA PRO ASP ILE ASP ILE TYR SEQRES 5 A 74 HIS CYS PRO ASN CYS GLU LYS THR HIS GLY LYS SER THR SEQRES 6 A 74 LEU LYS LYS LYS ARG THR TRP HIS LYS SEQRES 1 B 12 PRO ARG VAL M3L ALA ALA GLN ALA GLY ARG GLN SER MODRES 7M10 M3L B 4 LYS MODIFIED RESIDUE HET M3L B 4 12 HET ZN A 101 1 HET ZN A 102 1 HET FMT A 103 3 HET FMT A 104 3 HET FMT A 105 3 HET FMT A 106 3 HET FMT A 107 3 HET FMT B 501 3 HETNAM M3L N-TRIMETHYLLYSINE HETNAM ZN ZINC ION HETNAM FMT FORMIC ACID FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 3 ZN 2(ZN 2+) FORMUL 5 FMT 6(C H2 O2) FORMUL 11 HOH *124(H2 O) HELIX 1 AA1 GLY A 32 GLY A 36 1 5 HELIX 2 AA2 GLU A 38 PRO A 43 5 6 HELIX 3 AA3 CYS A 50 GLY A 58 1 9 SHEET 1 AA1 2 VAL A 6 TYR A 7 0 SHEET 2 AA1 2 LEU A 12 PRO A 13 -1 O LEU A 12 N TYR A 7 SHEET 1 AA2 3 TRP A 29 HIS A 31 0 SHEET 2 AA2 3 MET A 20 GLU A 22 -1 N ILE A 21 O PHE A 30 SHEET 3 AA2 3 VAL B 3 M3L B 4 -1 O M3L B 4 N MET A 20 SHEET 1 AA3 2 ILE A 45 ILE A 47 0 SHEET 2 AA3 2 THR A 61 LEU A 62 -1 O THR A 61 N ASP A 46 LINK C VAL B 3 N M3L B 4 1555 1555 1.33 LINK C M3L B 4 N ALA B 5 1555 1555 1.33 LINK SG CYS A 8 ZN ZN A 102 1555 1555 2.33 LINK SG CYS A 10 ZN ZN A 102 1555 1555 2.31 LINK SG CYS A 23 ZN ZN A 101 1555 1555 2.34 LINK SG CYS A 26 ZN ZN A 101 1555 1555 2.33 LINK ND1 HIS A 31 ZN ZN A 102 1555 1555 2.09 LINK SG CYS A 34 ZN ZN A 102 1555 1555 2.33 LINK SG CYS A 50 ZN ZN A 101 1555 1555 2.36 LINK SG CYS A 53 ZN ZN A 101 1555 1555 2.33 CRYST1 34.240 63.717 103.152 90.00 90.00 90.00 I 2 2 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 0.029206 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015694 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009694 0.00000