HEADER TRANSFERASE 20-APR-21 7OAT TITLE STRUCTURAL BASIS FOR TARGETED P97 REMODELLING BY ASPL AS PREREQUISITE TITLE 2 FOR P97 TRIMETHYLATION BY METTL21D COMPND MOL_ID: 1; COMPND 2 MOLECULE: TETHER CONTAINING UBX DOMAIN FOR GLUT4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALVEOLAR SOFT PART SARCOMA CHROMOSOMAL REGION CANDIDATE GENE COMPND 5 1 PROTEIN,ALVEOLAR SOFT PART SARCOMA LOCUS,RENAL PAPILLARY CELL COMPND 6 CARCINOMA PROTEIN 17,UBX DOMAIN-CONTAINING PROTEIN 9; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: TER ATPASE,15S MG(2+)-ATPASE P97 SUBUNIT,VALOSIN-CONTAINING COMPND 12 PROTEIN,VCP; COMPND 13 EC: 3.6.4.6; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: PROTEIN-LYSINE METHYLTRANSFERASE METTL21D; COMPND 17 CHAIN: C; COMPND 18 SYNONYM: METHYLTRANSFERASE-LIKE PROTEIN 21D,VCP LYSINE COMPND 19 METHYLTRANSFERASE,VCP-KMT,VALOSIN-CONTAINING PROTEIN LYSINE COMPND 20 METHYLTRANSFERASE; COMPND 21 EC: 2.1.1.-; COMPND 22 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: ASPSCR1, ASPL, RCC17, TUG, UBXD9, UBXN9; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: VCP; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: VCPKMT, C14ORF138, METTL21D; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS P97, AAA+ ATPASE, ASPL, METTL21D, VCP-KMT, VCP, METHYLATION, KEYWDS 2 REMODELLING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.PETROVIC,U.HEINEMANN,Y.ROSKE REVDAT 3 07-FEB-24 7OAT 1 REMARK REVDAT 2 15-FEB-23 7OAT 1 JRNL REVDAT 1 03-AUG-22 7OAT 0 JRNL AUTH S.PETROVIC,Y.ROSKE,B.RAMI,M.H.Q.PHAN,D.PANAKOVA,U.HEINEMANN JRNL TITL STRUCTURAL REMODELING OF AAA+ ATPASE P97 BY ADAPTOR PROTEIN JRNL TITL 2 ASPL FACILITATES POSTTRANSLATIONAL METHYLATION BY METTL21D. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 41120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 36656859 JRNL DOI 10.1073/PNAS.2208941120 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 (6-FEB-2020) REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 20828 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1042 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 51 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.40 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 417 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2744 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 396 REMARK 3 BIN R VALUE (WORKING SET) : 0.2729 REMARK 3 BIN FREE R VALUE : 0.3027 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.04 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 21 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6426 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 58 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 96.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 78.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.98570 REMARK 3 B22 (A**2) : -12.92860 REMARK 3 B33 (A**2) : 9.94290 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.55020 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.490 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.442 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.905 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.858 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 6614 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 8949 ; 6.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2369 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 1147 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 6614 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 859 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 4760 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 0.40 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.68 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 20.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|319 - A|496 } REMARK 3 ORIGIN FOR THE GROUP (A): 17.6841 27.1550 -48.0670 REMARK 3 T TENSOR REMARK 3 T11: -0.0891 T22: -0.0289 REMARK 3 T33: -0.1523 T12: -0.0148 REMARK 3 T13: 0.0006 T23: -0.0205 REMARK 3 L TENSOR REMARK 3 L11: 0.9848 L22: 1.4796 REMARK 3 L33: 3.7898 L12: 1.0917 REMARK 3 L13: -1.1548 L23: -1.6680 REMARK 3 S TENSOR REMARK 3 S11: 0.0053 S12: 0.1149 S13: 0.1216 REMARK 3 S21: 0.1491 S22: 0.0190 S23: 0.0698 REMARK 3 S31: -0.3109 S32: 0.0500 S33: -0.0243 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|23 - B|461 B|501 - B|503 } REMARK 3 ORIGIN FOR THE GROUP (A): 7.8403 -2.8869 -41.1784 REMARK 3 T TENSOR REMARK 3 T11: -0.2563 T22: -0.0375 REMARK 3 T33: -0.1622 T12: 0.1198 REMARK 3 T13: -0.0018 T23: 0.0265 REMARK 3 L TENSOR REMARK 3 L11: 1.0991 L22: 1.5475 REMARK 3 L33: 2.7729 L12: 0.9064 REMARK 3 L13: -0.8530 L23: -1.0690 REMARK 3 S TENSOR REMARK 3 S11: 0.0016 S12: -0.0856 S13: -0.1010 REMARK 3 S21: 0.0667 S22: -0.1461 S23: -0.0913 REMARK 3 S31: 0.1974 S32: 0.2639 S33: 0.1445 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { C|13 - C|223 C|301 - C|302 } REMARK 3 ORIGIN FOR THE GROUP (A): -16.4719 -20.3186 -1.5916 REMARK 3 T TENSOR REMARK 3 T11: -0.1479 T22: -0.2312 REMARK 3 T33: -0.2361 T12: -0.0032 REMARK 3 T13: 0.0369 T23: 0.0092 REMARK 3 L TENSOR REMARK 3 L11: 5.4631 L22: 4.2775 REMARK 3 L33: 5.4278 L12: 0.4893 REMARK 3 L13: 1.2598 L23: -0.9130 REMARK 3 S TENSOR REMARK 3 S11: -0.0500 S12: -0.2132 S13: -0.0190 REMARK 3 S21: 0.0009 S22: 0.0393 S23: -0.0042 REMARK 3 S31: 0.2615 S32: -0.1384 S33: 0.0106 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7OAT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-APR-21. REMARK 100 THE DEPOSITION ID IS D_1292111576. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-17 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20828 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.995 REMARK 200 RESOLUTION RANGE LOW (A) : 49.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 6.170 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.15 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 : 0.790 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: 5IFS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 8000, 0.2 M CALCIUM ACETATE, REMARK 280 0.1 M MES (PH 6.5), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 34.81100 REMARK 290 SMTRY3 2 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 311 REMARK 465 SER A 312 REMARK 465 VAL A 313 REMARK 465 ASP A 314 REMARK 465 ARG A 315 REMARK 465 GLU A 316 REMARK 465 PRO A 317 REMARK 465 VAL A 318 REMARK 465 GLN A 334 REMARK 465 ALA A 335 REMARK 465 GLU A 367 REMARK 465 GLU A 368 REMARK 465 ALA A 369 REMARK 465 PRO A 370 REMARK 465 LEU A 371 REMARK 465 ALA A 497 REMARK 465 ALA A 498 REMARK 465 GLY A 499 REMARK 465 SER A 500 REMARK 465 GLY B 0 REMARK 465 SER B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 GLY B 4 REMARK 465 ALA B 5 REMARK 465 ASP B 6 REMARK 465 SER B 7 REMARK 465 LYS B 8 REMARK 465 GLY B 9 REMARK 465 ASP B 10 REMARK 465 ASP B 11 REMARK 465 LEU B 12 REMARK 465 SER B 13 REMARK 465 THR B 14 REMARK 465 ALA B 15 REMARK 465 ILE B 16 REMARK 465 LEU B 17 REMARK 465 LYS B 18 REMARK 465 GLN B 19 REMARK 465 LYS B 20 REMARK 465 ASN B 21 REMARK 465 ARG B 22 REMARK 465 LEU B 429 REMARK 465 ILE B 430 REMARK 465 ASP B 431 REMARK 465 LEU B 432 REMARK 465 GLU B 433 REMARK 465 SER B 462 REMARK 465 ALA B 463 REMARK 465 LEU B 464 REMARK 465 ARG B 465 REMARK 465 GLU B 466 REMARK 465 THR B 467 REMARK 465 VAL B 468 REMARK 465 VAL B 469 REMARK 465 GLU B 470 REMARK 465 VAL B 471 REMARK 465 PRO B 472 REMARK 465 GLN B 473 REMARK 465 VAL B 474 REMARK 465 THR B 475 REMARK 465 TRP B 476 REMARK 465 GLU B 477 REMARK 465 ASP B 478 REMARK 465 ILE B 479 REMARK 465 GLY B 480 REMARK 465 GLY C 6 REMARK 465 SER C 7 REMARK 465 SER C 8 REMARK 465 LEU C 9 REMARK 465 GLU C 10 REMARK 465 ASP C 11 REMARK 465 PRO C 12 REMARK 465 LYS C 224 REMARK 465 SER C 225 REMARK 465 LYS C 226 REMARK 465 PHE C 227 REMARK 465 PRO C 228 REMARK 465 SER C 229 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 TRP A 336 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 336 CZ3 CH2 REMARK 470 LYS A 360 CG CD CE NZ REMARK 470 LYS B 148 CG CD CE NZ REMARK 470 LYS B 190 CG CD CE NZ REMARK 470 LYS B 236 CG CD CE NZ REMARK 470 LYS C 122 NZ REMARK 470 GLU C 149 CG CD OE1 OE2 REMARK 470 LYS C 160 NZ REMARK 470 LYS C 222 CG CD CE NZ REMARK 470 LYS C 223 CG CD CE NZ 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 M3L B 315 O - C - N ANGL. DEV. = 13.3 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 ASP A 328 35.36 -80.13 REMARK 500 LEU A 329 13.63 -140.47 REMARK 500 GLU A 331 -73.92 69.71 REMARK 500 LEU A 454 45.12 -96.59 REMARK 500 TYR A 471 -98.58 52.01 REMARK 500 TYR B 134 -60.96 -104.06 REMARK 500 LEU B 140 106.35 -46.75 REMARK 500 ASN B 296 59.55 -105.45 REMARK 500 ARG B 323 73.37 -107.67 REMARK 500 ARG B 362 -81.69 -65.40 REMARK 500 MET B 427 -111.05 62.42 REMARK 500 ASP C 96 -168.88 -173.65 REMARK 500 TYR C 147 -20.05 -165.55 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 MG B 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP B 503 O1G REMARK 620 2 ATP B 503 O3G 59.5 REMARK 620 N 1 DBREF 7OAT A 313 500 UNP Q9BZE9 ASPC1_HUMAN 313 500 DBREF 7OAT B 2 480 UNP P55072 TERA_HUMAN 2 480 DBREF 7OAT C 7 229 UNP Q9H867 MT21D_HUMAN 7 229 SEQADV 7OAT GLY A 311 UNP Q9BZE9 EXPRESSION TAG SEQADV 7OAT SER A 312 UNP Q9BZE9 EXPRESSION TAG SEQADV 7OAT GLY B 0 UNP P55072 EXPRESSION TAG SEQADV 7OAT SER B 1 UNP P55072 EXPRESSION TAG SEQADV 7OAT GLY C 6 UNP Q9H867 EXPRESSION TAG SEQRES 1 A 190 GLY SER VAL ASP ARG GLU PRO VAL ASP ARG GLU PRO VAL SEQRES 2 A 190 VAL CYS HIS PRO ASP LEU GLU GLU ARG LEU GLN ALA TRP SEQRES 3 A 190 PRO ALA GLU LEU PRO ASP GLU PHE PHE GLU LEU THR VAL SEQRES 4 A 190 ASP ASP VAL ARG ARG ARG LEU ALA GLN LEU LYS SER GLU SEQRES 5 A 190 ARG LYS ARG LEU GLU GLU ALA PRO LEU VAL THR LYS ALA SEQRES 6 A 190 PHE ARG GLU ALA GLN ILE LYS GLU LYS LEU GLU ARG TYR SEQRES 7 A 190 PRO LYS VAL ALA LEU ARG VAL LEU PHE PRO ASP ARG TYR SEQRES 8 A 190 VAL LEU GLN GLY PHE PHE ARG PRO SER GLU THR VAL GLY SEQRES 9 A 190 ASP LEU ARG ASP PHE VAL ARG SER HIS LEU GLY ASN PRO SEQRES 10 A 190 GLU LEU SER PHE TYR LEU PHE ILE THR PRO PRO LYS THR SEQRES 11 A 190 VAL LEU ASP ASP HIS THR GLN THR LEU PHE GLN ALA ASN SEQRES 12 A 190 LEU PHE PRO ALA ALA LEU VAL HIS LEU GLY ALA GLU GLU SEQRES 13 A 190 PRO ALA GLY VAL TYR LEU GLU PRO GLY LEU LEU GLU HIS SEQRES 14 A 190 ALA ILE SER PRO SER ALA ALA ASP VAL LEU VAL ALA ARG SEQRES 15 A 190 TYR MET SER ARG ALA ALA GLY SER SEQRES 1 B 481 GLY SER ALA SER GLY ALA ASP SER LYS GLY ASP ASP LEU SEQRES 2 B 481 SER THR ALA ILE LEU LYS GLN LYS ASN ARG PRO ASN ARG SEQRES 3 B 481 LEU ILE VAL ASP GLU ALA ILE ASN GLU ASP ASN SER VAL SEQRES 4 B 481 VAL SER LEU SER GLN PRO LYS MET ASP GLU LEU GLN LEU SEQRES 5 B 481 PHE ARG GLY ASP THR VAL LEU LEU LYS GLY LYS LYS ARG SEQRES 6 B 481 ARG GLU ALA VAL CYS ILE VAL LEU SER ASP ASP THR CYS SEQRES 7 B 481 SER ASP GLU LYS ILE ARG MET ASN ARG VAL VAL ARG ASN SEQRES 8 B 481 ASN LEU ARG VAL ARG LEU GLY ASP VAL ILE SER ILE GLN SEQRES 9 B 481 PRO CYS PRO ASP VAL LYS TYR GLY LYS ARG ILE HIS VAL SEQRES 10 B 481 LEU PRO ILE ASP ASP THR VAL GLU GLY ILE THR GLY ASN SEQRES 11 B 481 LEU PHE GLU VAL TYR LEU LYS PRO TYR PHE LEU GLU ALA SEQRES 12 B 481 TYR ARG PRO ILE ARG LYS GLY ASP ILE PHE LEU VAL ARG SEQRES 13 B 481 GLY GLY MET ARG ALA VAL GLU PHE LYS VAL VAL GLU THR SEQRES 14 B 481 ASP PRO SER PRO TYR CYS ILE VAL ALA PRO ASP THR VAL SEQRES 15 B 481 ILE HIS CYS GLU GLY GLU PRO ILE LYS ARG GLU ASP GLU SEQRES 16 B 481 GLU GLU SER LEU ASN GLU VAL GLY TYR ASP ASP ILE GLY SEQRES 17 B 481 GLY CYS ARG LYS GLN LEU ALA GLN ILE LYS GLU MET VAL SEQRES 18 B 481 GLU LEU PRO LEU ARG HIS PRO ALA LEU PHE LYS ALA ILE SEQRES 19 B 481 GLY VAL LYS PRO PRO ARG GLY ILE LEU LEU TYR GLY PRO SEQRES 20 B 481 PRO GLY THR GLY LYS THR LEU ILE ALA ARG ALA VAL ALA SEQRES 21 B 481 ASN GLU THR GLY ALA PHE PHE PHE LEU ILE ASN GLY PRO SEQRES 22 B 481 GLU ILE MET SER LYS LEU ALA GLY GLU SER GLU SER ASN SEQRES 23 B 481 LEU ARG LYS ALA PHE GLU GLU ALA GLU LYS ASN ALA PRO SEQRES 24 B 481 ALA ILE ILE PHE ILE ASP GLU LEU ASP ALA ILE ALA PRO SEQRES 25 B 481 LYS ARG GLU M3L THR HIS GLY GLU VAL GLU ARG ARG ILE SEQRES 26 B 481 VAL SER GLN LEU LEU THR LEU MET ASP GLY LEU LYS GLN SEQRES 27 B 481 ARG ALA HIS VAL ILE VAL MET ALA ALA THR ASN ARG PRO SEQRES 28 B 481 ASN SER ILE ASP PRO ALA LEU ARG ARG PHE GLY ARG PHE SEQRES 29 B 481 ASP ARG GLU VAL ASP ILE GLY ILE PRO ASP ALA THR GLY SEQRES 30 B 481 ARG LEU GLU ILE LEU GLN ILE HIS THR LYS ASN MET LYS SEQRES 31 B 481 LEU ALA ASP ASP VAL ASP LEU GLU GLN VAL ALA ASN GLU SEQRES 32 B 481 THR HIS GLY HIS VAL GLY ALA ASP LEU ALA ALA LEU CYS SEQRES 33 B 481 SER GLU ALA ALA LEU GLN ALA ILE ARG LYS LYS MET ASP SEQRES 34 B 481 LEU ILE ASP LEU GLU ASP GLU THR ILE ASP ALA GLU VAL SEQRES 35 B 481 MET ASN SER LEU ALA VAL THR MET ASP ASP PHE ARG TRP SEQRES 36 B 481 ALA LEU SER GLN SER ASN PRO SER ALA LEU ARG GLU THR SEQRES 37 B 481 VAL VAL GLU VAL PRO GLN VAL THR TRP GLU ASP ILE GLY SEQRES 1 C 224 GLY SER SER LEU GLU ASP PRO LEU ARG SER PHE VAL ARG SEQRES 2 C 224 VAL LEU GLU LYS ARG ASP GLY THR VAL LEU ARG LEU GLN SEQRES 3 C 224 GLN TYR SER SER GLY GLY VAL GLY CYS VAL VAL TRP ASP SEQRES 4 C 224 ALA ALA ILE VAL LEU SER LYS TYR LEU GLU THR PRO GLU SEQRES 5 C 224 PHE SER GLY ASP GLY ALA HIS ALA LEU SER ARG ARG SER SEQRES 6 C 224 VAL LEU GLU LEU GLY SER GLY THR GLY ALA VAL GLY LEU SEQRES 7 C 224 MET ALA ALA THR LEU GLY ALA ASP VAL VAL VAL THR ASP SEQRES 8 C 224 LEU GLU GLU LEU GLN ASP LEU LEU LYS MET ASN ILE ASN SEQRES 9 C 224 MET ASN LYS HIS LEU VAL THR GLY SER VAL GLN ALA LYS SEQRES 10 C 224 VAL LEU LYS TRP GLY GLU GLU ILE GLU GLY PHE PRO SER SEQRES 11 C 224 PRO PRO ASP PHE ILE LEU MET ALA ASP CYS ILE TYR TYR SEQRES 12 C 224 GLU GLU SER LEU GLU PRO LEU LEU LYS THR LEU LYS ASP SEQRES 13 C 224 ILE SER GLY PHE GLU THR CYS ILE ILE CYS CYS TYR GLU SEQRES 14 C 224 GLN ARG THR MET GLY LYS ASN PRO GLU ILE GLU LYS LYS SEQRES 15 C 224 TYR PHE GLU LEU LEU GLN LEU ASP PHE ASP PHE GLU LYS SEQRES 16 C 224 ILE PRO LEU GLU LYS HIS ASP GLU GLU TYR ARG SER GLU SEQRES 17 C 224 ASP ILE HIS ILE ILE TYR ILE ARG LYS LYS LYS SER LYS SEQRES 18 C 224 PHE PRO SER MODRES 7OAT M3L B 315 LYS MODIFIED RESIDUE HET M3L B 315 12 HET EDO B 501 4 HET EDO B 502 4 HET ATP B 503 31 HET MG B 504 1 HET EDO C 301 4 HET SAH C 302 26 HET EDO C 303 4 HETNAM M3L N-TRIMETHYLLYSINE HETNAM EDO 1,2-ETHANEDIOL HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 4 EDO 4(C2 H6 O2) FORMUL 6 ATP C10 H16 N5 O13 P3 FORMUL 7 MG MG 2+ FORMUL 9 SAH C14 H20 N6 O5 S FORMUL 11 HOH *58(H2 O) HELIX 1 AA1 HIS A 326 GLU A 330 5 5 HELIX 2 AA2 THR A 348 ARG A 365 1 18 HELIX 3 AA3 THR A 373 TYR A 388 1 16 HELIX 4 AA4 THR A 412 HIS A 423 1 12 HELIX 5 AA5 GLU A 473 HIS A 479 1 7 HELIX 6 AA6 SER A 482 ARG A 496 1 15 HELIX 7 AA7 GLN B 43 LEU B 49 1 7 HELIX 8 AA8 ASN B 85 ARG B 93 1 9 HELIX 9 AA9 ASP B 120 GLU B 124 5 5 HELIX 10 AB1 ASN B 129 TYR B 134 1 6 HELIX 11 AB2 TYR B 134 LEU B 140 1 7 HELIX 12 AB3 GLY B 202 ILE B 206 5 5 HELIX 13 AB4 CYS B 209 HIS B 226 1 18 HELIX 14 AB5 HIS B 226 GLY B 234 1 9 HELIX 15 AB6 GLY B 250 THR B 262 1 13 HELIX 16 AB7 GLY B 271 LYS B 277 1 7 HELIX 17 AB8 GLY B 280 ASN B 296 1 17 HELIX 18 AB9 GLU B 305 ALA B 310 1 6 HELIX 19 AC1 ARG B 323 GLY B 334 1 12 HELIX 20 AC2 ARG B 349 ILE B 353 5 5 HELIX 21 AC3 ASP B 354 ARG B 359 5 6 HELIX 22 AC4 ASP B 373 HIS B 384 1 12 HELIX 23 AC5 ASP B 395 GLU B 402 1 8 HELIX 24 AC6 VAL B 407 LYS B 426 1 20 HELIX 25 AC7 ALA B 439 SER B 444 1 6 HELIX 26 AC8 THR B 448 SER B 459 1 12 HELIX 27 AC9 GLY C 37 VAL C 41 5 5 HELIX 28 AD1 TRP C 43 GLU C 54 1 12 HELIX 29 AD2 THR C 55 GLY C 60 1 6 HELIX 30 AD3 GLY C 79 LEU C 88 1 10 HELIX 31 AD4 LEU C 97 GLU C 99 5 3 HELIX 32 AD5 LEU C 100 LYS C 112 1 13 HELIX 33 AD6 HIS C 113 VAL C 115 5 3 HELIX 34 AD7 TYR C 148 GLU C 153 1 6 HELIX 35 AD8 GLU C 153 SER C 163 1 11 HELIX 36 AD9 LYS C 180 GLN C 193 1 14 HELIX 37 AE1 PRO C 202 HIS C 206 5 5 SHEET 1 AA1 6 VAL A 323 CYS A 325 0 SHEET 2 AA1 6 VAL A 402 PHE A 407 -1 O GLN A 404 N VAL A 323 SHEET 3 AA1 6 VAL A 391 LEU A 396 -1 N LEU A 393 O GLY A 405 SHEET 4 AA1 6 ALA A 457 ALA A 464 1 O VAL A 460 N LEU A 396 SHEET 5 AA1 6 PHE A 431 ILE A 435 -1 N TYR A 432 O GLY A 463 SHEET 6 AA1 6 THR A 440 VAL A 441 -1 O THR A 440 N ILE A 435 SHEET 1 AA2 7 ASN B 24 ASP B 29 0 SHEET 2 AA2 7 LYS B 81 MET B 84 1 O ILE B 82 N ILE B 27 SHEET 3 AA2 7 VAL B 38 SER B 42 -1 N SER B 40 O ARG B 83 SHEET 4 AA2 7 GLU B 66 ASP B 74 1 O LEU B 72 N LEU B 41 SHEET 5 AA2 7 THR B 56 LYS B 60 -1 N LEU B 59 O ALA B 67 SHEET 6 AA2 7 VAL B 99 PRO B 104 -1 O SER B 101 N LYS B 60 SHEET 7 AA2 7 ASN B 24 ASP B 29 -1 N LEU B 26 O ILE B 100 SHEET 1 AA3 4 ILE B 151 GLY B 156 0 SHEET 2 AA3 4 ARG B 159 ASP B 169 -1 O PHE B 163 N PHE B 152 SHEET 3 AA3 4 ARG B 113 PRO B 118 -1 N HIS B 115 O GLU B 167 SHEET 4 AA3 4 VAL B 181 HIS B 183 1 O VAL B 181 N ILE B 114 SHEET 1 AA4 2 ILE B 126 THR B 127 0 SHEET 2 AA4 2 ILE B 437 ASP B 438 1 O ILE B 437 N THR B 127 SHEET 1 AA5 2 ARG B 144 ARG B 147 0 SHEET 2 AA5 2 TYR B 173 VAL B 176 -1 O VAL B 176 N ARG B 144 SHEET 1 AA6 5 PHE B 265 ASN B 270 0 SHEET 2 AA6 5 ALA B 299 ASP B 304 1 O PHE B 302 N ILE B 269 SHEET 3 AA6 5 VAL B 341 THR B 347 1 O MET B 344 N ILE B 301 SHEET 4 AA6 5 GLY B 240 TYR B 244 1 N LEU B 243 O ALA B 345 SHEET 5 AA6 5 PHE B 363 ASP B 368 1 O VAL B 367 N LEU B 242 SHEET 1 AA7 2 SER C 15 GLU C 21 0 SHEET 2 AA7 2 VAL C 27 TYR C 33 -1 O LEU C 30 N ARG C 18 SHEET 1 AA8 7 SER C 118 VAL C 123 0 SHEET 2 AA8 7 ASP C 91 ASP C 96 1 N VAL C 92 O SER C 118 SHEET 3 AA8 7 SER C 70 LEU C 74 1 N VAL C 71 O ASP C 91 SHEET 4 AA8 7 PHE C 139 ALA C 143 1 O PHE C 139 N LEU C 72 SHEET 5 AA8 7 CYS C 168 GLU C 174 1 O CYS C 172 N MET C 142 SHEET 6 AA8 7 ILE C 215 LYS C 222 -1 O ILE C 220 N ILE C 169 SHEET 7 AA8 7 PHE C 196 LYS C 200 -1 N GLU C 199 O TYR C 219 LINK C GLU B 314 N M3L B 315 1555 1555 1.34 LINK C M3L B 315 N THR B 316 1555 1555 1.36 LINK O1G ATP B 503 MG MG B 504 1555 1555 2.84 LINK O3G ATP B 503 MG MG B 504 1555 1555 2.15 CISPEP 1 THR A 436 PRO A 437 0 1.50 CISPEP 2 PRO A 437 PRO A 438 0 -3.79 CISPEP 3 PHE A 455 PRO A 456 0 -5.91 CISPEP 4 PRO B 106 ASP B 107 0 -2.87 CISPEP 5 ASP B 169 PRO B 170 0 7.68 CISPEP 6 SER B 171 PRO B 172 0 2.50 CISPEP 7 ALA B 297 PRO B 298 0 -4.94 CRYST1 54.258 69.622 140.175 90.00 94.41 90.00 P 1 21 1 2 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 0.018430 0.000000 0.001421 0.00000 SCALE2 0.000000 0.014363 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007155 0.00000