HEADER OXIDOREDUCTASE 06-MAY-20 6YYV
TITLE ASPARTYL/ASPARAGINYL BETA-HYDROXYLASE (ASPH) OXYGENASE AND TPR DOMAINS
TITLE 2 IN COMPLEX WITH MANGANESE AND 3-METHYL-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 16-OCT-24 6YYV 1 REMARK
REVDAT 3 07-FEB-24 6YYV 1 REMARK
REVDAT 2 19-JUL-23 6YYV 1 JRNL REMARK
REVDAT 1 17-MAR-21 6YYV 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. 1.77 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) : 1.77
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.62
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 72.8
REMARK 3 NUMBER OF REFLECTIONS : 43399
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.175
REMARK 3 R VALUE (WORKING SET) : 0.173
REMARK 3 FREE R VALUE : 0.208
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860
REMARK 3 FREE R VALUE TEST SET COUNT : 2111
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 43.6200 - 4.3700 1.00 4023 229 0.1577 0.1799
REMARK 3 2 4.3600 - 3.4700 1.00 3862 206 0.1384 0.1714
REMARK 3 3 3.4700 - 3.0300 1.00 3837 172 0.1745 0.2567
REMARK 3 4 3.0300 - 2.7500 1.00 3810 196 0.1864 0.2299
REMARK 3 5 2.7500 - 2.5500 1.00 3759 214 0.1913 0.2162
REMARK 3 6 2.5500 - 2.4000 1.00 3801 171 0.1793 0.2026
REMARK 3 7 2.4000 - 2.2800 1.00 3770 184 0.1879 0.2346
REMARK 3 8 2.2800 - 2.1800 1.00 3743 191 0.1995 0.2273
REMARK 3 9 2.1800 - 2.1000 0.99 3709 190 0.2133 0.2635
REMARK 3 10 2.1000 - 2.0300 0.76 2818 144 0.2302 0.2871
REMARK 3 11 2.0300 - 1.9600 0.55 2050 114 0.2392 0.2506
REMARK 3 12 1.9600 - 1.9100 0.35 1323 63 0.2664 0.3512
REMARK 3 13 1.9100 - 1.8600 0.14 523 23 0.2722 0.2051
REMARK 3 14 1.8600 - 1.8100 0.05 175 8 0.2735 0.2853
REMARK 3 15 1.8100 - 1.7700 0.02 85 6 0.2732 0.3435
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) : 0.169
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.569
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 32.09
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.66
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 : 0.012 3511
REMARK 3 ANGLE : 1.150 4759
REMARK 3 CHIRALITY : 0.058 503
REMARK 3 PLANARITY : 0.009 625
REMARK 3 DIHEDRAL : 21.720 1307
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 4
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 330 THROUGH 374 )
REMARK 3 ORIGIN FOR THE GROUP (A): -13.5945 8.8338 -72.8512
REMARK 3 T TENSOR
REMARK 3 T11: 1.5714 T22: 1.4150
REMARK 3 T33: 0.7967 T12: 0.3257
REMARK 3 T13: 0.4638 T23: -0.2939
REMARK 3 L TENSOR
REMARK 3 L11: 1.8041 L22: 4.2111
REMARK 3 L33: 1.5047 L12: 0.6795
REMARK 3 L13: 1.4866 L23: 0.5497
REMARK 3 S TENSOR
REMARK 3 S11: 0.2220 S12: 1.1464 S13: -0.0731
REMARK 3 S21: -1.7111 S22: -0.0149 S23: -1.0737
REMARK 3 S31: 0.2401 S32: 0.6261 S33: -0.4329
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 375 THROUGH 517 )
REMARK 3 ORIGIN FOR THE GROUP (A): -24.4963 7.2486 -49.4543
REMARK 3 T TENSOR
REMARK 3 T11: 0.4329 T22: 0.1295
REMARK 3 T33: 0.2566 T12: 0.0412
REMARK 3 T13: 0.0093 T23: -0.0446
REMARK 3 L TENSOR
REMARK 3 L11: 1.2056 L22: 2.0175
REMARK 3 L33: 1.2447 L12: -0.4206
REMARK 3 L13: 0.3165 L23: -1.1106
REMARK 3 S TENSOR
REMARK 3 S11: 0.1398 S12: 0.2479 S13: 0.0439
REMARK 3 S21: -0.5281 S22: -0.1455 S23: -0.2057
REMARK 3 S31: 0.2519 S32: -0.0047 S33: -0.0197
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 518 THROUGH 593 )
REMARK 3 ORIGIN FOR THE GROUP (A): -6.9092 -0.3439 -24.2585
REMARK 3 T TENSOR
REMARK 3 T11: 0.2340 T22: 0.2011
REMARK 3 T33: 0.2357 T12: 0.0243
REMARK 3 T13: 0.0006 T23: -0.0724
REMARK 3 L TENSOR
REMARK 3 L11: 1.8832 L22: 0.8847
REMARK 3 L33: 1.3360 L12: 0.4142
REMARK 3 L13: 0.6631 L23: 0.5763
REMARK 3 S TENSOR
REMARK 3 S11: 0.0149 S12: -0.0591 S13: -0.2268
REMARK 3 S21: -0.1050 S22: 0.1347 S23: -0.1147
REMARK 3 S31: 0.1471 S32: 0.1944 S33: -0.1017
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 594 THROUGH 758 )
REMARK 3 ORIGIN FOR THE GROUP (A): -6.0049 13.4003 -13.1720
REMARK 3 T TENSOR
REMARK 3 T11: 0.1597 T22: 0.2566
REMARK 3 T33: 0.2033 T12: 0.0104
REMARK 3 T13: -0.0031 T23: -0.0848
REMARK 3 L TENSOR
REMARK 3 L11: 2.3553 L22: 1.0017
REMARK 3 L33: 0.9924 L12: 0.1914
REMARK 3 L13: 0.2205 L23: 0.6225
REMARK 3 S TENSOR
REMARK 3 S11: 0.0089 S12: -0.3585 S13: 0.2743
REMARK 3 S21: -0.1519 S22: 0.0272 S23: -0.0407
REMARK 3 S31: -0.1186 S32: 0.0257 S33: -0.0527
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 6YYV 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_1292107208.
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 : 7.9
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 : 43399
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770
REMARK 200 RESOLUTION RANGE LOW (A) : 87.240
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2
REMARK 200 DATA REDUNDANCY : 13.30
REMARK 200 R MERGE (I) : 0.11000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 1.87600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> 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: PHASER
REMARK 200 STARTING MODEL: 5JZA
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 59.49
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM MAGNESIUM ACETATE TETRAHYDRATE,
REMARK 280 20% W/V PEG 3350, 1 MM MANGANESE CHLORIDE, 2 MM 3-METHYL-2-
REMARK 280 OXOGLUTARATE, 18 MG/ML PROTEIN, PH 7.9, 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 24.40100
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 87.24400
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.26050
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 87.24400
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.40100
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.26050
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: 130 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19950 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 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 330 CG CD CE NZ
REMARK 470 LYS A 336 CG CD CE NZ
REMARK 470 ASP A 338 CG OD1 OD2
REMARK 470 ILE A 341 CG1 CG2 CD1
REMARK 470 LEU A 345 CG CD1 CD2
REMARK 470 LYS A 350 CG CD CE NZ
REMARK 470 ARG A 354 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 356 CG CD CE NZ
REMARK 470 ILE A 357 CG1 CG2 CD1
REMARK 470 GLU A 358 CG CD OE1 OE2
REMARK 470 GLU A 359 CG CD OE1 OE2
REMARK 470 VAL A 361 CG1 CG2
REMARK 470 LYS A 365 CG CD CE NZ
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 GLN A 373 OE1 NE2
REMARK 470 LYS A 391 CG CD CE NZ
REMARK 470 ARG A 392 NE CZ NH1 NH2
REMARK 470 GLU A 396 CG CD OE1 OE2
REMARK 470 ASP A 417 CG OD1 OD2
REMARK 470 LYS A 424 CD CE NZ
REMARK 470 LYS A 541 CG CD CE NZ
REMARK 470 LYS A 697 CG CD CE NZ
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 353 CE NZ
REMARK 480 ASN A 362 CG OD1 ND2
REMARK 480 ARG A 393 NE CZ NH1 NH2
REMARK 480 LYS A 420 NZ
REMARK 480 LYS A 579 CD CE NZ
REMARK 480 LYS A 607 CD CE NZ
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 OE1 GLU A 621 HD1 HIS A 675 1.55
REMARK 500 O LEU A 367 H TYR A 371 1.57
REMARK 500 O HOH A 1154 O HOH A 1165 1.60
REMARK 500 O HOH A 902 O HOH A 930 1.69
REMARK 500 O HOH A 906 O HOH A 1178 1.76
REMARK 500 O HOH A 1038 O HOH A 1091 1.82
REMARK 500 O HOH A 989 O HOH A 1242 1.85
REMARK 500 O HOH A 1268 O HOH A 1294 1.86
REMARK 500 O HOH A 1107 O HOH A 1146 1.87
REMARK 500 O HOH A 1207 O HOH A 1231 1.89
REMARK 500 O HOH A 1165 O HOH A 1273 1.90
REMARK 500 O HOH A 1111 O HOH A 1117 1.96
REMARK 500 O HOH A 1130 O HOH A 1267 1.99
REMARK 500 O HOH A 926 O HOH A 974 1.99
REMARK 500 O HOH A 1294 O HOH A 1304 2.01
REMARK 500 O HOH A 1124 O HOH A 1267 2.02
REMARK 500 O HOH A 976 O HOH A 1103 2.08
REMARK 500 O HOH A 971 O HOH A 1199 2.08
REMARK 500 O HOH A 1154 O HOH A 1273 2.09
REMARK 500 O HOH A 1097 O HOH A 1227 2.10
REMARK 500 O HOH A 1247 O HOH A 1300 2.10
REMARK 500 O HOH A 1250 O HOH A 1274 2.11
REMARK 500 O HOH A 1151 O HOH A 1243 2.11
REMARK 500 O HOH A 1124 O HOH A 1130 2.12
REMARK 500 O HOH A 1119 O HOH A 1136 2.12
REMARK 500 O HOH A 1067 O HOH A 1129 2.12
REMARK 500 O HOH A 1213 O HOH A 1247 2.13
REMARK 500 O HOH A 1050 O HOH A 1266 2.14
REMARK 500 O HOH A 908 O HOH A 1012 2.15
REMARK 500 O HOH A 1162 O HOH A 1212 2.17
REMARK 500 O HOH A 1131 O HOH A 1187 2.17
REMARK 500 OE2 GLU A 585 O HOH A 901 2.18
REMARK 500 O HOH A 918 O HOH A 1250 2.19
REMARK 500 O LEU A 367 N TYR A 371 2.19
REMARK 500 O HOH A 908 O HOH A 1080 2.19
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 1172 O HOH A 1229 3454 2.02
REMARK 500 O HOH A 1192 O HOH A 1229 3454 2.13
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 469 77.09 -101.38
REMARK 500 TYR A 583 52.45 -92.29
REMARK 500 ALA A 608 53.49 -119.14
REMARK 500 ALA A 705 -125.73 56.89
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 A1304 DISTANCE = 5.97 ANGSTROMS
REMARK 525 HOH A1305 DISTANCE = 7.05 ANGSTROMS
REMARK 525 HOH A1306 DISTANCE = 7.39 ANGSTROMS
REMARK 525 HOH A1307 DISTANCE = 8.14 ANGSTROMS
REMARK 525 HOH A1308 DISTANCE = 8.23 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 86.3
REMARK 620 3 Q1Z A 802 O01 85.8 96.0
REMARK 620 4 Q1Z A 802 O02 157.8 93.1 72.2
REMARK 620 5 HOH A 997 O 102.7 92.0 168.7 99.5
REMARK 620 6 HOH A1115 O 93.7 177.5 86.5 87.9 85.5
REMARK 620 N 1 2 3 4 5
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 Q1Z A 802
DBREF 6YYV 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 Q1Z A 802 17
HETNAM MN MANGANESE (II) ION
HETNAM Q1Z (3~{R})-3-METHYL-2-OXIDANYLIDENE-PENTANEDIOIC ACID
FORMUL 2 MN MN 2+
FORMUL 3 Q1Z C6 H8 O5
FORMUL 4 HOH *408(H2 O)
HELIX 1 AA1 PHE A 337 THR A 340 5 4
HELIX 2 AA2 ILE A 341 GLY A 355 1 15
HELIX 3 AA3 LYS A 356 ARG A 369 1 14
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 GLY A 518 1 16
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 GLU A 652 1 9
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 GLU A 621
SHEET 3 AA3 5 HIS A 725 GLN A 729 -1 O GLN A 729 N THR A 674
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 2.05
LINK NE2 HIS A 679 MN MN A 801 1555 1555 2.15
LINK NE2 HIS A 725 MN MN A 801 1555 1555 2.16
LINK MN MN A 801 O01 Q1Z A 802 1555 1555 2.20
LINK MN MN A 801 O02 Q1Z A 802 1555 1555 2.20
LINK MN MN A 801 O HOH A 997 1555 1555 2.10
LINK MN MN A 801 O HOH A1115 1555 1555 2.17
SITE 1 AC1 5 HIS A 679 HIS A 725 Q1Z A 802 HOH A 997
SITE 2 AC1 5 HOH A1115
SITE 1 AC2 12 TRP A 625 SER A 668 MET A 670 HIS A 679
SITE 2 AC2 12 ARG A 688 HIS A 690 HIS A 725 VAL A 727
SITE 3 AC2 12 ARG A 735 ILE A 737 MN A 801 HOH A1115
CRYST1 48.802 70.521 174.488 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 0.020491 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014180 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005731 0.00000