HEADER OXIDOREDUCTASE 06-MAY-20 6YYU TITLE ASPARTYL/ASPARAGINYL BETA-HYDROXYLASE (ASPH) OXYGENASE AND TPR DOMAINS TITLE 2 IN COMPLEX WITH MANGANESE AND 2-OXOGLUTARATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASPARTYL/ASPARAGINYL BETA-HYDROXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ASPARTATE BETA-HYDROXYLASE,ASP BETA-HYDROXYLASE,PEPTIDE- COMPND 5 ASPARTATE BETA-DIOXYGENASE; COMPND 6 EC: 1.14.11.16; COMPND 7 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: ASPH, BAH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ASPARTYL/ASPARAGINYL BETA-HYDROXYLASE, DIOXYGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.NAKASHIMA,L.BREWITZ,C.J.SCHOFIELD REVDAT 4 23-OCT-24 6YYU 1 REMARK REVDAT 3 07-FEB-24 6YYU 1 REMARK REVDAT 2 19-JUL-23 6YYU 1 JRNL REMARK REVDAT 1 17-MAR-21 6YYU 0 JRNL AUTH L.BREWITZ,Y.NAKASHIMA,C.J.SCHOFIELD JRNL TITL SYNTHESIS OF 2-OXOGLUTARATE DERIVATIVES AND THEIR EVALUATION JRNL TITL 2 AS COSUBSTRATES AND INHIBITORS OF HUMAN JRNL TITL 3 ASPARTATE/ASPARAGINE-BETA-HYDROXYLASE. JRNL REF CHEM SCI V. 12 1327 2020 JRNL REFN ISSN 2041-6520 JRNL PMID 34163896 JRNL DOI 10.1039/D0SC04301J REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 85.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 59.0 REMARK 3 NUMBER OF REFLECTIONS : 20452 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1064 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 85.4400 - 4.2200 1.00 4310 264 0.1698 0.1865 REMARK 3 2 4.2200 - 3.3500 0.88 3689 180 0.1724 0.2196 REMARK 3 3 3.3500 - 2.9200 1.00 4106 223 0.2347 0.2767 REMARK 3 4 2.9200 - 2.6600 0.92 3739 221 0.2839 0.3267 REMARK 3 5 2.6600 - 2.4700 0.54 2208 113 0.3006 0.3046 REMARK 3 6 2.4700 - 2.3200 0.22 895 39 0.3093 0.2697 REMARK 3 7 2.3200 - 2.2000 0.09 357 19 0.3421 0.3425 REMARK 3 8 2.2000 - 2.1100 0.02 84 5 0.3453 0.4302 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.231 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.80 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 : 0.017 3410 REMARK 3 ANGLE : 1.619 4630 REMARK 3 CHIRALITY : 0.068 496 REMARK 3 PLANARITY : 0.010 609 REMARK 3 DIHEDRAL : 21.800 1237 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 6YYU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1292107395. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97623 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20459 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 200 RESOLUTION RANGE LOW (A) : 85.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : 0.18500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.74600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 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: 5JZA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES SODIUM, 10% V/V 2 REMARK 280 -PROPANOL, 20% W/V PEG 4000, 1 MM MANGANESE CHLORIDE, 2 MM 2- REMARK 280 OXOGLUTARATE, 18 MG/ML PROTEIN, PH 7.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K 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 24.39550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 85.43500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.00150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 85.43500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.39550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.00150 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL 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 LYS A 330 REMARK 465 ILE A 758 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 332 CG CD CE NZ REMARK 470 LEU A 334 CG CD1 CD2 REMARK 470 ASN A 335 CG OD1 ND2 REMARK 470 LYS A 336 CG CD CE NZ REMARK 470 PHE A 337 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 338 CG OD1 OD2 REMARK 470 LYS A 339 CG CD CE NZ REMARK 470 THR A 340 OG1 CG2 REMARK 470 LYS A 342 CG CD CE NZ REMARK 470 GLU A 344 CG CD OE1 OE2 REMARK 470 ASP A 346 CG OD1 OD2 REMARK 470 GLU A 349 CG CD OE1 OE2 REMARK 470 LYS A 350 CG CD CE NZ REMARK 470 LEU A 351 CG CD1 CD2 REMARK 470 LYS A 353 CG CD CE NZ REMARK 470 ARG A 354 CZ NH1 NH2 REMARK 470 LYS A 356 CG CD CE NZ REMARK 470 ILE A 357 CG1 CG2 CD1 REMARK 470 GLU A 359 CG CD OE1 OE2 REMARK 470 VAL A 361 CG1 CG2 REMARK 470 GLU A 366 CG CD OE1 OE2 REMARK 470 ARG A 369 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 370 CG CD CE NZ REMARK 470 TYR A 371 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 373 CG CD OE1 NE2 REMARK 470 SER A 374 OG REMARK 470 GLN A 383 OE1 NE2 REMARK 470 LEU A 388 CG CD1 CD2 REMARK 470 GLU A 390 CG CD OE1 OE2 REMARK 470 LYS A 391 CD CE NZ REMARK 470 ARG A 392 NE CZ NH1 NH2 REMARK 470 ARG A 393 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 413 CG OD1 OD2 REMARK 470 LYS A 424 CG CD CE NZ REMARK 470 GLN A 448 CG CD OE1 NE2 REMARK 470 LYS A 541 CG CD CE NZ REMARK 470 LYS A 545 CG CD CE NZ REMARK 470 LYS A 609 CG CD CE NZ REMARK 470 ARG A 635 CD NE CZ NH1 NH2 REMARK 470 LYS A 642 CE NZ REMARK 470 LYS A 653 CG CD CE NZ REMARK 470 LYS A 697 CG CD CE NZ REMARK 470 ASP A 730 CG OD1 OD2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 552 CE NZ REMARK 480 GLN A 632 CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ILE A 357 H VAL A 361 1.47 REMARK 500 O LEU A 367 H TYR A 371 1.47 REMARK 500 O ASN A 335 H LYS A 339 1.53 REMARK 500 HE ARG A 562 O HOH A 903 1.58 REMARK 500 O GLU A 366 H LYS A 370 1.59 REMARK 500 MN MN A 801 O1 AKG A 802 1.62 REMARK 500 O HOH A 965 O HOH A 976 1.93 REMARK 500 O HOH A 987 O HOH A 990 1.93 REMARK 500 O HOH A 902 O HOH A 931 1.99 REMARK 500 O HOH A 940 O HOH A 966 2.12 REMARK 500 O ASN A 335 N LYS A 339 2.13 REMARK 500 O HOH A 930 O HOH A 962 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 918 O HOH A 973 4555 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 384 CB CYS A 384 SG -0.124 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 429 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 533 CB - CG - OD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 537 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP A 616 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 MET A 670 CG - SD - CE ANGL. DEV. = -10.2 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 THR A 340 41.45 -87.43 REMARK 500 LYS A 356 50.02 -100.32 REMARK 500 LEU A 411 140.57 -31.35 REMARK 500 LYS A 503 57.56 -94.36 REMARK 500 TYR A 583 46.48 -88.81 REMARK 500 ALA A 608 63.34 -159.31 REMARK 500 ALA A 644 73.75 -116.01 REMARK 500 LYS A 653 5.02 -67.36 REMARK 500 PRO A 672 150.26 -46.91 REMARK 500 ALA A 705 -121.45 44.17 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 A 993 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A 994 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A 995 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH A 996 DISTANCE = 8.01 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 MN A 801 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 679 NE2 REMARK 620 2 HIS A 725 NE2 84.3 REMARK 620 3 AKG A 802 O5 97.2 94.0 REMARK 620 4 HOH A 905 O 96.1 89.2 166.6 REMARK 620 5 HOH A 937 O 85.5 165.1 98.0 81.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG A 802 DBREF 6YYU A 330 758 UNP Q12797 ASPH_HUMAN 330 758 SEQRES 1 A 429 LYS PRO LYS LEU LEU ASN LYS PHE ASP LYS THR ILE LYS SEQRES 2 A 429 ALA GLU LEU ASP ALA ALA GLU LYS LEU ARG LYS ARG GLY SEQRES 3 A 429 LYS ILE GLU GLU ALA VAL ASN ALA PHE LYS GLU LEU VAL SEQRES 4 A 429 ARG LYS TYR PRO GLN SER PRO ARG ALA ARG TYR GLY LYS SEQRES 5 A 429 ALA GLN CYS GLU ASP ASP LEU ALA GLU LYS ARG ARG SER SEQRES 6 A 429 ASN GLU VAL LEU ARG GLY ALA ILE GLU THR TYR GLN GLU SEQRES 7 A 429 VAL ALA SER LEU PRO ASP VAL PRO ALA ASP LEU LEU LYS SEQRES 8 A 429 LEU SER LEU LYS ARG ARG SER ASP ARG GLN GLN PHE LEU SEQRES 9 A 429 GLY HIS MET ARG GLY SER LEU LEU THR LEU GLN ARG LEU SEQRES 10 A 429 VAL GLN LEU PHE PRO ASN ASP THR SER LEU LYS ASN ASP SEQRES 11 A 429 LEU GLY VAL GLY TYR LEU LEU ILE GLY ASP ASN ASP ASN SEQRES 12 A 429 ALA LYS LYS VAL TYR GLU GLU VAL LEU SER VAL THR PRO SEQRES 13 A 429 ASN ASP GLY PHE ALA LYS VAL HIS TYR GLY PHE ILE LEU SEQRES 14 A 429 LYS ALA GLN ASN LYS ILE ALA GLU SER ILE PRO TYR LEU SEQRES 15 A 429 LYS GLU GLY ILE GLU SER GLY ASP PRO GLY THR ASP ASP SEQRES 16 A 429 GLY ARG PHE TYR PHE HIS LEU GLY ASP ALA MET GLN ARG SEQRES 17 A 429 VAL GLY ASN LYS GLU ALA TYR LYS TRP TYR GLU LEU GLY SEQRES 18 A 429 HIS LYS ARG GLY HIS PHE ALA SER VAL TRP GLN ARG SER SEQRES 19 A 429 LEU TYR ASN VAL ASN GLY LEU LYS ALA GLN PRO TRP TRP SEQRES 20 A 429 THR PRO LYS GLU THR GLY TYR THR GLU LEU VAL LYS SER SEQRES 21 A 429 LEU GLU ARG ASN TRP LYS LEU ILE ARG ASP GLU GLY LEU SEQRES 22 A 429 ALA VAL MET ASP LYS ALA LYS GLY LEU PHE LEU PRO GLU SEQRES 23 A 429 ASP GLU ASN LEU ARG GLU LYS GLY ASP TRP SER GLN PHE SEQRES 24 A 429 THR LEU TRP GLN GLN GLY ARG ARG ASN GLU ASN ALA CYS SEQRES 25 A 429 LYS GLY ALA PRO LYS THR CYS THR LEU LEU GLU LYS PHE SEQRES 26 A 429 PRO GLU THR THR GLY CYS ARG ARG GLY GLN ILE LYS TYR SEQRES 27 A 429 SER ILE MET HIS PRO GLY THR HIS VAL TRP PRO HIS THR SEQRES 28 A 429 GLY PRO THR ASN CYS ARG LEU ARG MET HIS LEU GLY LEU SEQRES 29 A 429 VAL ILE PRO LYS GLU GLY CYS LYS ILE ARG CYS ALA ASN SEQRES 30 A 429 GLU THR LYS THR TRP GLU GLU GLY LYS VAL LEU ILE PHE SEQRES 31 A 429 ASP ASP SER PHE GLU HIS GLU VAL TRP GLN ASP ALA SER SEQRES 32 A 429 SER PHE ARG LEU ILE PHE ILE VAL ASP VAL TRP HIS PRO SEQRES 33 A 429 GLU LEU THR PRO GLN GLN ARG ARG SER LEU PRO ALA ILE HET MN A 801 1 HET AKG A 802 14 HETNAM MN MANGANESE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID FORMUL 2 MN MN 2+ FORMUL 3 AKG C5 H6 O5 FORMUL 4 HOH *96(H2 O) HELIX 1 AA1 ASN A 335 THR A 340 1 6 HELIX 2 AA2 ILE A 341 ARG A 354 1 14 HELIX 3 AA3 LYS A 356 TYR A 371 1 16 HELIX 4 AA4 SER A 374 ARG A 393 1 20 HELIX 5 AA5 SER A 394 LEU A 411 1 18 HELIX 6 AA6 PRO A 415 GLY A 434 1 20 HELIX 7 AA7 HIS A 435 PHE A 450 1 16 HELIX 8 AA8 ASP A 453 ILE A 467 1 15 HELIX 9 AA9 ASP A 469 THR A 484 1 16 HELIX 10 AB1 ASP A 487 GLN A 501 1 15 HELIX 11 AB2 LYS A 503 SER A 517 1 15 HELIX 12 AB3 ASP A 524 VAL A 538 1 15 HELIX 13 AB4 GLY A 539 LYS A 541 5 3 HELIX 14 AB5 GLU A 542 ARG A 553 1 12 HELIX 15 AB6 THR A 577 GLY A 582 1 6 HELIX 16 AB7 TYR A 583 ASN A 593 1 11 HELIX 17 AB8 ASN A 593 ALA A 608 1 16 HELIX 18 AB9 LYS A 609 PHE A 612 5 4 HELIX 19 AC1 ASN A 637 ALA A 644 1 8 HELIX 20 AC2 ALA A 644 LYS A 653 1 10 HELIX 21 AC3 PHE A 654 GLY A 659 1 6 HELIX 22 AC4 THR A 748 LEU A 755 1 8 SHEET 1 AA1 7 TRP A 575 TRP A 576 0 SHEET 2 AA1 7 VAL A 716 PHE A 719 -1 O ILE A 718 N TRP A 576 SHEET 3 AA1 7 ARG A 686 VAL A 694 -1 N ARG A 688 O PHE A 719 SHEET 4 AA1 7 ARG A 735 TRP A 743 -1 O PHE A 738 N LEU A 691 SHEET 5 AA1 7 GLN A 664 MET A 670 -1 N LYS A 666 O ILE A 739 SHEET 6 AA1 7 TRP A 625 GLN A 632 -1 N LEU A 630 O ILE A 665 SHEET 7 AA1 7 LEU A 613 PRO A 614 -1 N LEU A 613 O GLN A 627 SHEET 1 AA2 7 TRP A 575 TRP A 576 0 SHEET 2 AA2 7 VAL A 716 PHE A 719 -1 O ILE A 718 N TRP A 576 SHEET 3 AA2 7 ARG A 686 VAL A 694 -1 N ARG A 688 O PHE A 719 SHEET 4 AA2 7 ARG A 735 TRP A 743 -1 O PHE A 738 N LEU A 691 SHEET 5 AA2 7 GLN A 664 MET A 670 -1 N LYS A 666 O ILE A 739 SHEET 6 AA2 7 TRP A 625 GLN A 632 -1 N LEU A 630 O ILE A 665 SHEET 7 AA2 7 ARG A 635 ARG A 636 -1 O ARG A 635 N GLN A 632 SHEET 1 AA3 5 ARG A 620 LYS A 622 0 SHEET 2 AA3 5 THR A 674 HIS A 679 -1 O HIS A 675 N LYS A 622 SHEET 3 AA3 5 HIS A 725 GLN A 729 -1 O VAL A 727 N VAL A 676 SHEET 4 AA3 5 CYS A 700 CYS A 704 -1 N ARG A 703 O GLU A 726 SHEET 5 AA3 5 GLU A 707 LYS A 709 -1 O LYS A 709 N ILE A 702 SSBOND 1 CYS A 641 CYS A 648 1555 1555 2.03 LINK NE2 HIS A 679 MN MN A 801 1555 1555 2.25 LINK NE2 HIS A 725 MN MN A 801 1555 1555 2.09 LINK MN MN A 801 O5 AKG A 802 1555 1555 2.51 LINK MN MN A 801 O HOH A 905 1555 1555 2.14 LINK MN MN A 801 O HOH A 937 1555 1555 2.42 SITE 1 AC1 5 HIS A 679 HIS A 725 AKG A 802 HOH A 905 SITE 2 AC1 5 HOH A 937 SITE 1 AC2 10 TRP A 625 SER A 668 HIS A 679 ARG A 688 SITE 2 AC2 10 HIS A 690 HIS A 725 ARG A 735 MN A 801 SITE 3 AC2 10 HOH A 905 HOH A 937 CRYST1 48.791 70.003 170.870 90.00 90.00 90.00 P 21 21 21 4 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 0.020496 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014285 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005852 0.00000