HEADER PROTEIN BINDING 29-NOV-22 8HL6 TITLE CRYSTAL STRUCTURE OF HUMAN VALOSIN-CONTAINING PROTEIN TITLE 2 METHYLTRANSFERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN N-LYSINE METHYLTRANSFERASE METTL21D; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: METHYLTRANSFERASE-LIKE PROTEIN 21D; COMPND 5 EC: 2.1.1.-; COMPND 6 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: METTL21D; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VCPKMT, METHYLTRANSFERASE, ASPL, ASPSCR1, UBXD9, TUG, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR W.KANG,J.K.YANG REVDAT 3 29-MAY-24 8HL6 1 REMARK REVDAT 2 02-AUG-23 8HL6 1 JRNL REVDAT 1 12-JUL-23 8HL6 0 JRNL AUTH T.Q.NGUYEN,S.KOH,J.KWON,S.JANG,W.KANG,J.K.YANG JRNL TITL STRUCTURAL BASIS FOR RECOGNITION AND METHYLATION OF P97 BY JRNL TITL 2 METTL21D, A VALOSIN-CONTAINING PROTEIN LYSINE JRNL TITL 3 METHYLTRANSFERASE. JRNL REF ISCIENCE V. 26 07222 2023 JRNL REFN ESSN 2589-0042 JRNL PMID 37456834 JRNL DOI 10.1016/J.ISCI.2023.107222 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2-4158 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 23334 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1146 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 32.7480 - 3.5987 1.00 3056 153 0.1605 0.1867 REMARK 3 2 3.5987 - 2.8569 1.00 2916 164 0.1927 0.2201 REMARK 3 3 2.8569 - 2.4959 1.00 2857 165 0.2050 0.2513 REMARK 3 4 2.4959 - 2.2678 1.00 2883 135 0.2048 0.2454 REMARK 3 5 2.2678 - 2.1053 1.00 2855 124 0.2247 0.2810 REMARK 3 6 2.1053 - 1.9811 0.99 2810 143 0.2428 0.3010 REMARK 3 7 1.9811 - 1.8819 0.91 2551 128 0.2924 0.3489 REMARK 3 8 1.8819 - 1.8000 0.81 2260 134 0.3350 0.3664 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.500 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 : 0.007 1698 REMARK 3 ANGLE : 0.923 2297 REMARK 3 CHIRALITY : 0.057 260 REMARK 3 PLANARITY : 0.005 290 REMARK 3 DIHEDRAL : 3.626 1020 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -25.7010 6.4623 8.3012 REMARK 3 T TENSOR REMARK 3 T11: 0.2700 T22: 0.2341 REMARK 3 T33: 0.2798 T12: 0.0163 REMARK 3 T13: 0.0608 T23: 0.0057 REMARK 3 L TENSOR REMARK 3 L11: 2.9456 L22: 3.9825 REMARK 3 L33: 3.4990 L12: 0.7419 REMARK 3 L13: -1.2475 L23: -1.4537 REMARK 3 S TENSOR REMARK 3 S11: -0.0194 S12: 0.0387 S13: -0.0129 REMARK 3 S21: -0.2619 S22: -0.1278 S23: -0.3060 REMARK 3 S31: 0.1384 S32: 0.0959 S33: 0.1081 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 8HL6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1300033828. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23428 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 64.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 % PEG 1000, 0.1 M NA/K PHOSPHATE REMARK 280 (PH 6.2), AND 0.2M SODIUM CHLORIDE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.09700 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 86.19400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 86.19400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 43.09700 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 ASP A 3 REMARK 465 THR A 4 REMARK 465 LEU A 5 REMARK 465 GLU A 6 REMARK 465 SER A 7 REMARK 465 SER A 8 REMARK 465 LEU A 9 REMARK 465 GLU A 10 REMARK 465 ASP A 11 REMARK 465 PRO A 12 REMARK 465 LEU A 13 REMARK 465 ARG A 14 REMARK 465 SER A 15 REMARK 465 PRO A 228 REMARK 465 SER A 229 REMARK 465 HIS A 230 REMARK 465 HIS A 231 REMARK 465 HIS A 232 REMARK 465 HIS A 233 REMARK 465 HIS A 234 REMARK 465 HIS A 235 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 VAL A 38 CG1 CG2 REMARK 470 ASP A 61 CG OD1 OD2 REMARK 470 ARG A 68 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 149 CG CD OE1 OE2 REMARK 470 GLU A 150 CG CD OE1 OE2 REMARK 470 THR A 177 OG1 CG2 REMARK 470 MET A 178 CG SD CE REMARK 470 LYS A 187 CG CD CE NZ REMARK 470 LEU A 191 CG CD1 CD2 REMARK 470 LEU A 194 CG CD1 CD2 REMARK 470 GLU A 208 CG CD OE1 OE2 REMARK 470 GLU A 213 CD OE1 OE2 REMARK 470 LYS A 223 CG CD CE NZ 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 ASP A 61 30.86 -85.75 REMARK 500 ASP A 96 -168.42 -171.73 REMARK 500 GLU A 131 111.07 -39.29 REMARK 500 TYR A 147 30.15 -90.97 REMARK 500 LYS A 224 74.68 -155.55 REMARK 500 REMARK 500 REMARK: NULL DBREF 8HL6 A 1 229 UNP Q9H867 MT21D_HUMAN 1 229 SEQADV 8HL6 HIS A 230 UNP Q9H867 EXPRESSION TAG SEQADV 8HL6 HIS A 231 UNP Q9H867 EXPRESSION TAG SEQADV 8HL6 HIS A 232 UNP Q9H867 EXPRESSION TAG SEQADV 8HL6 HIS A 233 UNP Q9H867 EXPRESSION TAG SEQADV 8HL6 HIS A 234 UNP Q9H867 EXPRESSION TAG SEQADV 8HL6 HIS A 235 UNP Q9H867 EXPRESSION TAG SEQRES 1 A 235 MET ALA ASP THR LEU GLU SER SER LEU GLU ASP PRO LEU SEQRES 2 A 235 ARG SER PHE VAL ARG VAL LEU GLU LYS ARG ASP GLY THR SEQRES 3 A 235 VAL LEU ARG LEU GLN GLN TYR SER SER GLY GLY VAL GLY SEQRES 4 A 235 CYS VAL VAL TRP ASP ALA ALA ILE VAL LEU SER LYS TYR SEQRES 5 A 235 LEU GLU THR PRO GLU PHE SER GLY ASP GLY ALA HIS ALA SEQRES 6 A 235 LEU SER ARG ARG SER VAL LEU GLU LEU GLY SER GLY THR SEQRES 7 A 235 GLY ALA VAL GLY LEU MET ALA ALA THR LEU GLY ALA ASP SEQRES 8 A 235 VAL VAL VAL THR ASP LEU GLU GLU LEU GLN ASP LEU LEU SEQRES 9 A 235 LYS MET ASN ILE ASN MET ASN LYS HIS LEU VAL THR GLY SEQRES 10 A 235 SER VAL GLN ALA LYS VAL LEU LYS TRP GLY GLU GLU ILE SEQRES 11 A 235 GLU GLY PHE PRO SER PRO PRO ASP PHE ILE LEU MET ALA SEQRES 12 A 235 ASP CYS ILE TYR TYR GLU GLU SER LEU GLU PRO LEU LEU SEQRES 13 A 235 LYS THR LEU LYS ASP ILE SER GLY PHE GLU THR CYS ILE SEQRES 14 A 235 ILE CYS CYS TYR GLU GLN ARG THR MET GLY LYS ASN PRO SEQRES 15 A 235 GLU ILE GLU LYS LYS TYR PHE GLU LEU LEU GLN LEU ASP SEQRES 16 A 235 PHE ASP PHE GLU LYS ILE PRO LEU GLU LYS HIS ASP GLU SEQRES 17 A 235 GLU TYR ARG SER GLU ASP ILE HIS ILE ILE TYR ILE ARG SEQRES 18 A 235 LYS LYS LYS SER LYS PHE PRO SER HIS HIS HIS HIS HIS SEQRES 19 A 235 HIS HET SAM A 301 27 HETNAM SAM S-ADENOSYLMETHIONINE FORMUL 2 SAM C15 H22 N6 O5 S FORMUL 3 HOH *96(H2 O) HELIX 1 AA1 TRP A 43 GLU A 54 1 12 HELIX 2 AA2 THR A 55 SER A 59 5 5 HELIX 3 AA3 GLY A 79 LEU A 88 1 10 HELIX 4 AA4 LEU A 97 GLU A 99 5 3 HELIX 5 AA5 LEU A 100 LYS A 112 1 13 HELIX 6 AA6 HIS A 113 VAL A 115 5 3 HELIX 7 AA7 TYR A 148 GLU A 150 5 3 HELIX 8 AA8 SER A 151 SER A 163 1 13 HELIX 9 AA9 LYS A 180 ASP A 195 1 16 HELIX 10 AB1 PRO A 202 HIS A 206 5 5 SHEET 1 AA1 2 VAL A 17 GLU A 21 0 SHEET 2 AA1 2 VAL A 27 GLN A 31 -1 O LEU A 30 N ARG A 18 SHEET 1 AA2 7 SER A 118 VAL A 123 0 SHEET 2 AA2 7 ASP A 91 ASP A 96 1 N VAL A 92 O SER A 118 SHEET 3 AA2 7 SER A 70 GLU A 73 1 N GLU A 73 O VAL A 93 SHEET 4 AA2 7 PHE A 139 ALA A 143 1 O LEU A 141 N LEU A 72 SHEET 5 AA2 7 CYS A 168 GLU A 174 1 O CYS A 172 N MET A 142 SHEET 6 AA2 7 ILE A 215 LYS A 222 -1 O ILE A 220 N ILE A 169 SHEET 7 AA2 7 PHE A 196 LYS A 200 -1 N ASP A 197 O ARG A 221 CRYST1 58.170 58.170 129.291 90.00 90.00 120.00 P 31 2 1 6 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 0.017191 0.009925 0.000000 0.00000 SCALE2 0.000000 0.019851 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007734 0.00000