HEADER HYDROLASE, TRANSFERASE 19-NOV-19 6V0T TITLE CRYSTAL STRUCTURE OF CATALYTIC SUBUNIT OF BOVINE PYRUVATE TITLE 2 DEHYDROGENASE PHOSPHATASE 1 - CATALYTIC DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: [PYRUVATE DEHYDROGENASE [ACETYL-TRANSFERRING]]-PHOSPHATASE COMPND 3 1, MITOCHONDRIAL; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: PDP 1,PROTEIN PHOSPHATASE 2C,PYRUVATE DEHYDROGENASE COMPND 6 PHOSPHATASE CATALYTIC SUBUNIT 1,PDPC 1; COMPND 7 EC: 3.1.3.43 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS PYRUVATE DEHYDROGENASE PHOSPHATASE, PYRUVATE DEHYDROGENASE, KEYWDS 2 TRANSFERASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.GUO,W.QIU,S.R.ERNST,D.W.CARROLL,M.L.HACKERT REVDAT 3 11-OCT-23 6V0T 1 LINK REVDAT 2 15-JUL-20 6V0T 1 JRNL REVDAT 1 18-DEC-19 6V0T 0 SPRSDE 18-DEC-19 6V0T 3N3C JRNL AUTH Y.GUO,W.QIU,T.E.ROCHE,M.L.HACKERT JRNL TITL CRYSTAL STRUCTURE OF THE CATALYTIC SUBUNIT OF BOVINE JRNL TITL 2 PYRUVATE DEHYDROGENASE PHOSPHATASE. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 76 292 2020 JRNL REFN ESSN 2053-230X JRNL PMID 32627744 JRNL DOI 10.1107/S2053230X20007943 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16-3549 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 33298 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.360 REMARK 3 FREE R VALUE TEST SET COUNT : 2784 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 52.1170 - 5.6980 0.98 1677 157 0.2531 0.2540 REMARK 3 2 5.6980 - 4.5235 1.00 1605 158 0.1888 0.1960 REMARK 3 3 4.5235 - 3.9519 1.00 1581 139 0.1753 0.2064 REMARK 3 4 3.9519 - 3.5907 1.00 1595 143 0.1982 0.2440 REMARK 3 5 3.5907 - 3.3333 1.00 1560 149 0.2156 0.2313 REMARK 3 6 3.3333 - 3.1368 1.00 1573 119 0.2122 0.2343 REMARK 3 7 3.1368 - 2.9798 1.00 1587 126 0.2236 0.2437 REMARK 3 8 2.9798 - 2.8501 1.00 1535 157 0.2154 0.2675 REMARK 3 9 2.8501 - 2.7404 1.00 1558 145 0.2236 0.2730 REMARK 3 10 2.7404 - 2.6458 1.00 1551 145 0.2378 0.2695 REMARK 3 11 2.6458 - 2.5631 1.00 1513 162 0.2338 0.2781 REMARK 3 12 2.5631 - 2.4898 1.00 1539 149 0.2290 0.2887 REMARK 3 13 2.4898 - 2.4243 1.00 1523 145 0.2370 0.2880 REMARK 3 14 2.4243 - 2.3651 1.00 1534 137 0.2433 0.2832 REMARK 3 15 2.3651 - 2.3113 1.00 1568 142 0.2319 0.2852 REMARK 3 16 2.3113 - 2.2622 1.00 1524 145 0.2426 0.2836 REMARK 3 17 2.2622 - 2.2169 0.99 1505 119 0.2886 0.3312 REMARK 3 18 2.2169 - 2.1751 0.92 1434 125 0.2669 0.3068 REMARK 3 19 2.1751 - 2.1362 0.86 1335 120 0.2759 0.3274 REMARK 3 20 2.1362 - 2.1000 0.81 1217 102 0.2683 0.3023 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.29 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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: REMARK 3 REFINEMENT WAS PERFORMED WITH PHENIX VERSION 1.16-3549. REMARK 3 REMARK 3 REFINEMENT STRATEGY: XYZ (RECIPROCAL-SPACE, XYZ (REAL SPACE, REMARK 3 OCCUPANCIES. REMARK 3 REMARK 3 TARGETS AND WEIGHTING, OPTIMIZE X-RAY/STEREOCHEMNISTRY WEIGHT. REMARK 3 USE SECONDARY STRUCTURE. REMARK 4 REMARK 4 6V0T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1000244465. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-02 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 : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97900 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33626 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 52.117 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 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) : 0.33000 REMARK 200 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: 1A6Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE PROTEIN SOLUTION WAS 20MG/ML IN 10 REMARK 280 MM TRIS-HCL, PH 7.3, 50 MM NACL, 1MM MNSO4, 2MM DTT, AND 1MM REMARK 280 BENZAMIDE. THE WELL SOLUTION (MIXED 1:1) CONTAINED 0.10M HEPES, REMARK 280 PH 7.5 AND 20% JEFFAMINE M-600., HANGING DROP, TEMPERATURE 298K, REMARK 280 EVAPORATION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 115.50333 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 57.75167 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 57.75167 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 115.50333 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 ALA A 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 PRO A 4 REMARK 465 GLN A 5 REMARK 465 LYS A 6 REMARK 465 PHE A 7 REMARK 465 TYR A 8 REMARK 465 LEU A 9 REMARK 465 THR A 153 REMARK 465 GLY A 154 REMARK 465 GLU A 155 REMARK 465 SER A 156 REMARK 465 THR A 157 REMARK 465 ASP A 158 REMARK 465 ASP A 303 REMARK 465 GLN A 304 REMARK 465 LEU A 305 REMARK 465 ASN A 306 REMARK 465 ASP A 307 REMARK 465 ASN A 308 REMARK 465 GLU A 309 REMARK 465 TYR A 310 REMARK 465 THR A 311 REMARK 465 HIS A 370 REMARK 465 HIS A 371 REMARK 465 GLN A 372 REMARK 465 GLN A 373 REMARK 465 PRO A 374 REMARK 465 ILE A 375 REMARK 465 ALA A 376 REMARK 465 VAL A 377 REMARK 465 GLY A 378 REMARK 465 GLY A 379 REMARK 465 TYR A 380 REMARK 465 LYS A 381 REMARK 465 VAL A 382 REMARK 465 THR A 383 REMARK 465 LEU A 384 REMARK 465 GLY A 385 REMARK 465 GLN A 386 REMARK 465 MET A 387 REMARK 465 HIS A 388 REMARK 465 GLY A 389 REMARK 465 LEU A 390 REMARK 465 LEU A 391 REMARK 465 THR A 392 REMARK 465 GLU A 393 REMARK 465 ARG A 394 REMARK 465 ARG A 395 REMARK 465 ALA A 396 REMARK 465 LYS A 397 REMARK 465 MET A 398 REMARK 465 SER A 399 REMARK 465 SER A 400 REMARK 465 VAL A 401 REMARK 465 PHE A 402 REMARK 465 GLU A 403 REMARK 465 VAL A 424 REMARK 465 ASP A 425 REMARK 465 HIS A 426 REMARK 465 ASN A 464 REMARK 465 GLN A 465 REMARK 465 GLU A 466 REMARK 465 GLN A 467 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 THR A 10 OG1 CG2 REMARK 470 GLN A 13 CG CD OE1 NE2 REMARK 470 VAL A 14 CG1 CG2 REMARK 470 ASN A 15 CG OD1 ND2 REMARK 470 SER A 16 OG REMARK 470 LYS A 19 CG CD CE NZ REMARK 470 LYS A 33 CG CD CE NZ REMARK 470 ARG A 65 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 100 CG CD OE1 OE2 REMARK 470 ASN A 107 CG OD1 ND2 REMARK 470 VAL A 109 CG1 CG2 REMARK 470 GLU A 110 CG CD OE1 OE2 REMARK 470 SER A 111 OG REMARK 470 ARG A 113 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 131 CG CD CE NZ REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 LEU A 151 CG CD1 CD2 REMARK 470 ILE A 159 CG1 CG2 CD1 REMARK 470 GLU A 230 CG CD OE1 OE2 REMARK 470 GLN A 246 CG CD OE1 NE2 REMARK 470 ARG A 249 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 260 CG CD CE NZ REMARK 470 LYS A 264 CG CD CE NZ REMARK 470 LYS A 268 CG CD CE NZ REMARK 470 LYS A 295 CG CD CE NZ REMARK 470 GLU A 299 CG CD OE1 OE2 REMARK 470 SER A 300 OG REMARK 470 LYS A 312 CG CD CE NZ REMARK 470 THR A 331 OG1 CG2 REMARK 470 GLN A 356 CG CD OE1 NE2 REMARK 470 MET A 369 CG SD CE REMARK 470 GLN A 405 CG CD OE1 NE2 REMARK 470 ASN A 419 CG OD1 ND2 REMARK 470 PHE A 421 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 431 CG CD CE NZ REMARK 470 GLU A 437 CG CD OE1 OE2 REMARK 470 GLU A 438 CG CD OE1 OE2 REMARK 470 LEU A 439 CG CD1 CD2 REMARK 470 TYR A 462 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 463 CG 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 HOH A 740 O HOH A 812 2.07 REMARK 500 O HOH A 729 O HOH A 749 2.16 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 PRO A 259 170.26 -58.98 REMARK 500 LEU A 275 -62.00 -123.10 REMARK 500 PHE A 421 36.11 70.52 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 826 DISTANCE = 5.94 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 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 73 OD1 REMARK 620 2 GLY A 74 O 92.9 REMARK 620 3 HOH A 601 O 175.2 84.0 REMARK 620 4 HOH A 613 O 84.3 94.6 92.3 REMARK 620 5 HOH A 685 O 90.3 173.4 93.2 91.4 REMARK 620 6 HOH A 740 O 91.7 95.1 92.2 169.7 79.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 502 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 73 OD2 REMARK 620 2 ASP A 347 OD1 82.5 REMARK 620 3 ASP A 445 OD2 165.0 94.6 REMARK 620 4 HOH A 610 O 95.3 86.4 99.2 REMARK 620 5 HOH A 667 O 82.7 96.7 83.1 176.0 REMARK 620 6 HOH A 685 O 104.5 169.4 80.6 85.0 92.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 505 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 410 NE2 REMARK 620 2 HIS A 414 NE2 106.2 REMARK 620 3 HOH A 622 O 59.7 126.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 506 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SO4 A 503 O4 REMARK 620 2 HOH A 626 O 43.0 REMARK 620 N 1 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 507 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3N3C RELATED DB: PDB REMARK 900 THE NEW STRUCTURE WAS A RESULT OF FURTHER REFINEMENT WITH PHENIX DBREF 6V0T A 1 467 UNP P35816 PDP1_BOVIN 72 538 SEQRES 1 A 467 ALA SER THR PRO GLN LYS PHE TYR LEU THR PRO PRO GLN SEQRES 2 A 467 VAL ASN SER ILE LEU LYS ALA ASN GLU TYR SER PHE LYS SEQRES 3 A 467 VAL PRO GLU PHE ASP GLY LYS ASN VAL SER SER VAL LEU SEQRES 4 A 467 GLY PHE ASP SER ASN GLN LEU PRO ALA ASN ALA PRO ILE SEQRES 5 A 467 GLU ASP ARG ARG SER ALA ALA THR CYS LEU GLN THR ARG SEQRES 6 A 467 GLY MET LEU LEU GLY VAL PHE ASP GLY HIS ALA GLY CYS SEQRES 7 A 467 ALA CYS SER GLN ALA VAL SER GLU ARG LEU PHE TYR TYR SEQRES 8 A 467 ILE ALA VAL SER LEU LEU PRO HIS GLU THR LEU LEU GLU SEQRES 9 A 467 ILE GLU ASN ALA VAL GLU SER GLY ARG ALA LEU LEU PRO SEQRES 10 A 467 ILE LEU GLN TRP HIS LYS HIS PRO ASN ASP TYR PHE SER SEQRES 11 A 467 LYS GLU ALA SER LYS LEU TYR PHE ASN SER LEU ARG THR SEQRES 12 A 467 TYR TRP GLN GLU LEU ILE ASP LEU ASN THR GLY GLU SER SEQRES 13 A 467 THR ASP ILE ASP VAL LYS GLU ALA LEU ILE ASN ALA PHE SEQRES 14 A 467 LYS ARG LEU ASP ASN ASP ILE SER LEU GLU ALA GLN VAL SEQRES 15 A 467 GLY ASP PRO ASN SER PHE LEU ASN TYR LEU VAL LEU ARG SEQRES 16 A 467 VAL ALA PHE SER GLY ALA THR ALA CYS VAL ALA HIS VAL SEQRES 17 A 467 ASP GLY VAL ASP LEU HIS VAL ALA ASN THR GLY ASP SER SEQRES 18 A 467 ARG ALA MET LEU GLY VAL GLN GLU GLU ASP GLY SER TRP SEQRES 19 A 467 SER ALA VAL THR LEU SER ASN ASP HIS ASN ALA GLN ASN SEQRES 20 A 467 GLU ARG GLU VAL GLU ARG LEU LYS LEU GLU HIS PRO LYS SEQRES 21 A 467 ASN GLU ALA LYS SER VAL VAL LYS GLN ASP ARG LEU LEU SEQRES 22 A 467 GLY LEU LEU MET PRO PHE ARG ALA PHE GLY ASP VAL LYS SEQRES 23 A 467 PHE LYS TRP SER ILE ASP LEU GLN LYS ARG VAL ILE GLU SEQRES 24 A 467 SER GLY PRO ASP GLN LEU ASN ASP ASN GLU TYR THR LYS SEQRES 25 A 467 PHE ILE PRO PRO ASN TYR TYR THR PRO PRO TYR LEU THR SEQRES 26 A 467 ALA GLU PRO GLU VAL THR TYR HIS ARG LEU ARG PRO GLN SEQRES 27 A 467 ASP LYS PHE LEU VAL LEU ALA THR ASP GLY LEU TRP GLU SEQRES 28 A 467 THR MET HIS ARG GLN ASP VAL VAL ARG ILE VAL GLY GLU SEQRES 29 A 467 TYR LEU THR GLY MET HIS HIS GLN GLN PRO ILE ALA VAL SEQRES 30 A 467 GLY GLY TYR LYS VAL THR LEU GLY GLN MET HIS GLY LEU SEQRES 31 A 467 LEU THR GLU ARG ARG ALA LYS MET SER SER VAL PHE GLU SEQRES 32 A 467 ASP GLN ASN ALA ALA THR HIS LEU ILE ARG HIS ALA VAL SEQRES 33 A 467 GLY ASN ASN GLU PHE GLY ALA VAL ASP HIS GLU ARG LEU SEQRES 34 A 467 SER LYS MET LEU SER LEU PRO GLU GLU LEU ALA ARG MET SEQRES 35 A 467 TYR ARG ASP ASP ILE THR ILE ILE VAL VAL GLN PHE ASN SEQRES 36 A 467 SER HIS VAL VAL GLY ALA TYR GLN ASN GLN GLU GLN HET MN A 501 1 HET MN A 502 1 HET SO4 A 503 5 HET SO4 A 504 5 HET MN A 505 1 HET MN A 506 1 HET MN A 507 1 HETNAM MN MANGANESE (II) ION HETNAM SO4 SULFATE ION FORMUL 2 MN 5(MN 2+) FORMUL 4 SO4 2(O4 S 2-) FORMUL 9 HOH *226(H2 O) HELIX 1 AA1 THR A 10 LYS A 19 1 10 HELIX 2 AA2 CYS A 78 LEU A 96 1 19 HELIX 3 AA3 PRO A 98 GLY A 112 1 15 HELIX 4 AA4 ALA A 133 ASN A 152 1 20 HELIX 5 AA5 ASP A 160 GLY A 183 1 24 HELIX 6 AA6 ASN A 186 SER A 199 1 14 HELIX 7 AA7 ASN A 247 GLU A 257 1 11 HELIX 8 AA8 PRO A 259 ALA A 263 5 5 HELIX 9 AA9 VAL A 285 LYS A 288 5 4 HELIX 10 AB1 SER A 290 GLU A 299 1 10 HELIX 11 AB2 THR A 346 GLU A 351 1 6 HELIX 12 AB3 HIS A 354 THR A 367 1 14 HELIX 13 AB4 ASN A 406 GLY A 417 1 12 HELIX 14 AB5 ARG A 428 SER A 434 1 7 HELIX 15 AB6 PRO A 436 ARG A 444 1 9 HELIX 16 AB7 ASN A 455 GLN A 463 1 9 SHEET 1 AA1 6 TYR A 23 LYS A 26 0 SHEET 2 AA1 6 VAL A 38 LEU A 46 -1 O SER A 43 N TYR A 23 SHEET 3 AA1 6 ILE A 447 PHE A 454 -1 O VAL A 451 N ASP A 42 SHEET 4 AA1 6 ASP A 339 ALA A 345 -1 N LEU A 342 O VAL A 452 SHEET 5 AA1 6 ARG A 222 GLN A 228 -1 N MET A 224 O VAL A 343 SHEET 6 AA1 6 TRP A 234 THR A 238 -1 O VAL A 237 N LEU A 225 SHEET 1 AA2 5 LEU A 119 TRP A 121 0 SHEET 2 AA2 5 ASP A 54 CYS A 61 -1 N THR A 60 O GLN A 120 SHEET 3 AA2 5 MET A 67 HIS A 75 -1 O LEU A 68 N ALA A 59 SHEET 4 AA2 5 GLY A 200 ALA A 201 -1 O GLY A 200 N HIS A 75 SHEET 5 AA2 5 PHE A 282 GLY A 283 -1 O PHE A 282 N ALA A 201 SHEET 1 AA3 6 LEU A 119 TRP A 121 0 SHEET 2 AA3 6 ASP A 54 CYS A 61 -1 N THR A 60 O GLN A 120 SHEET 3 AA3 6 MET A 67 HIS A 75 -1 O LEU A 68 N ALA A 59 SHEET 4 AA3 6 ALA A 203 ASP A 209 -1 O ALA A 206 N LEU A 69 SHEET 5 AA3 6 ASP A 212 THR A 218 -1 O HIS A 214 N HIS A 207 SHEET 6 AA3 6 GLU A 329 ARG A 334 -1 O GLU A 329 N ASN A 217 SHEET 1 AA4 2 VAL A 267 LYS A 268 0 SHEET 2 AA4 2 ARG A 271 LEU A 272 -1 O ARG A 271 N LYS A 268 LINK OD1 ASP A 73 MN MN A 501 1555 1555 2.11 LINK OD2 ASP A 73 MN MN A 502 1555 1555 2.11 LINK O GLY A 74 MN MN A 501 1555 1555 2.17 LINK OD1 ASP A 292 MN MN A 507 1555 6765 1.97 LINK OD1 ASP A 347 MN MN A 502 1555 1555 2.15 LINK NE2 HIS A 410 MN MN A 505 1555 1555 2.34 LINK NE2 HIS A 414 MN MN A 505 1555 1555 2.15 LINK OD2 ASP A 445 MN MN A 502 1555 1555 2.12 LINK MN MN A 501 O HOH A 601 1555 1555 2.36 LINK MN MN A 501 O HOH A 613 1555 1555 2.34 LINK MN MN A 501 O HOH A 685 1555 1555 2.30 LINK MN MN A 501 O HOH A 740 1555 1555 2.13 LINK MN MN A 502 O HOH A 610 1555 1555 2.02 LINK MN MN A 502 O HOH A 667 1555 1555 2.24 LINK MN MN A 502 O HOH A 685 1555 1555 2.17 LINK O4 SO4 A 503 MN MN A 506 1555 6765 2.02 LINK MN MN A 505 O HOH A 622 1555 1555 2.67 LINK MN MN A 506 O HOH A 626 1555 1555 2.65 CISPEP 1 PRO A 321 PRO A 322 0 1.66 SITE 1 AC1 6 ASP A 73 GLY A 74 HOH A 601 HOH A 613 SITE 2 AC1 6 HOH A 685 HOH A 740 SITE 1 AC2 6 ASP A 73 ASP A 347 ASP A 445 HOH A 610 SITE 2 AC2 6 HOH A 667 HOH A 685 SITE 1 AC3 5 SER A 290 ILE A 291 ASP A 292 SO4 A 504 SITE 2 AC3 5 MN A 506 SITE 1 AC4 4 ILE A 291 ASP A 292 SO4 A 503 MN A 507 SITE 1 AC5 3 HIS A 410 HIS A 414 HOH A 622 SITE 1 AC6 6 SER A 290 ILE A 291 PRO A 321 SO4 A 503 SITE 2 AC6 6 HOH A 626 HOH A 779 SITE 1 AC7 2 ASP A 292 SO4 A 504 CRYST1 75.339 75.339 173.255 90.00 90.00 120.00 P 32 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 0.013273 0.007663 0.000000 0.00000 SCALE2 0.000000 0.015327 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005772 0.00000