HEADER TRANSFERASE 04-SEP-15 5DKU TITLE C-TERMINAL HIS TAGGED APPOL EXONUCLEASE MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PREX DNA POLYMERASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1389-2016; COMPND 5 SYNONYM: PFPREX; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM (ISOLATE 3D7); SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: ISOLATE 3D7; SOURCE 5 GENE: POM1, PF14_0112; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL-21 GEN-X KEYWDS DNA POLYMERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.E.MILTON,R.B.HONZATKO,J.Y.CHOE,S.W.NELSON REVDAT 4 27-SEP-23 5DKU 1 JRNL REMARK LINK REVDAT 3 19-OCT-16 5DKU 1 JRNL REVDAT 2 17-AUG-16 5DKU 1 JRNL REVDAT 1 10-AUG-16 5DKU 0 JRNL AUTH M.E.MILTON,J.Y.CHOE,R.B.HONZATKO,S.W.NELSON JRNL TITL CRYSTAL STRUCTURE OF THE APICOPLAST DNA POLYMERASE FROM JRNL TITL 2 PLASMODIUM FALCIPARUM: THE FIRST LOOK AT A PLASTIDIC JRNL TITL 3 A-FAMILY DNA POLYMERASE. JRNL REF J.MOL.BIOL. V. 428 3920 2016 JRNL REFN ESSN 1089-8638 JRNL PMID 27487482 JRNL DOI 10.1016/J.JMB.2016.07.016 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2148: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 44271 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.530 REMARK 3 FREE R VALUE TEST SET COUNT : 2007 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 47.9213 - 6.9810 0.97 3015 140 0.1767 0.2262 REMARK 3 2 6.9810 - 5.5437 0.99 3036 149 0.2030 0.2347 REMARK 3 3 5.5437 - 4.8437 1.00 3039 145 0.1507 0.1881 REMARK 3 4 4.8437 - 4.4012 1.00 3039 142 0.1412 0.1665 REMARK 3 5 4.4012 - 4.0859 1.00 3028 138 0.1501 0.1670 REMARK 3 6 4.0859 - 3.8451 0.99 3022 150 0.1741 0.2110 REMARK 3 7 3.8451 - 3.6526 1.00 3019 139 0.1931 0.2453 REMARK 3 8 3.6526 - 3.4937 1.00 3029 148 0.2031 0.2730 REMARK 3 9 3.4937 - 3.3592 0.99 3016 145 0.2192 0.2470 REMARK 3 10 3.3592 - 3.2433 1.00 3014 144 0.2405 0.2740 REMARK 3 11 3.2433 - 3.1419 1.00 3028 145 0.2520 0.2893 REMARK 3 12 3.1419 - 3.0521 0.99 2989 140 0.2564 0.3292 REMARK 3 13 3.0521 - 2.9718 0.99 3031 139 0.2776 0.3177 REMARK 3 14 2.9718 - 2.8993 0.98 2959 143 0.2967 0.3556 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.33 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 : 0.002 9839 REMARK 3 ANGLE : 0.477 13255 REMARK 3 CHIRALITY : 0.043 1483 REMARK 3 PLANARITY : 0.002 1685 REMARK 3 DIHEDRAL : 12.757 6063 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 5DKU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213331. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-15 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 : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44314 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.52600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MR-ROSETTA REMARK 200 STARTING MODEL: 5DKT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM ACETATE TETRAHYDRATE, REMARK 280 0.1 M SODIUM CACODYLATE TRHYDRATE PH 6.5, 30% W/V POLYETHYLENE REMARK 280 GLYCOL 4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 110.44733 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 55.22367 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 82.83550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 27.61183 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 138.05917 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 284 REMARK 465 LYS A 285 REMARK 465 LEU A 286 REMARK 465 LYS A 287 REMARK 465 ASP A 288 REMARK 465 GLU A 289 REMARK 465 ASN A 290 REMARK 465 ILE A 291 REMARK 465 ASN A 292 REMARK 465 VAL A 293 REMARK 465 ASN A 294 REMARK 465 SER A 295 REMARK 465 GLN A 296 REMARK 465 GLN A 297 REMARK 465 GLN A 298 REMARK 465 VAL A 299 REMARK 465 LEU A 300 REMARK 465 LYS A 301 REMARK 465 ALA A 302 REMARK 465 LEU A 303 REMARK 465 GLN A 304 REMARK 465 LYS A 305 REMARK 465 ASN A 306 REMARK 465 ASN A 307 REMARK 465 VAL A 308 REMARK 465 ARG A 309 REMARK 465 ASP A 310 REMARK 465 ILE A 311 REMARK 465 SER A 312 REMARK 465 ASN A 313 REMARK 465 LYS A 314 REMARK 465 LEU A 315 REMARK 465 ILE A 316 REMARK 465 GLU A 317 REMARK 465 ASN A 318 REMARK 465 THR A 319 REMARK 465 SER A 320 REMARK 465 ASP A 321 REMARK 465 SER A 322 REMARK 465 ASN A 323 REMARK 465 LEU A 324 REMARK 465 LYS A 325 REMARK 465 ASN A 326 REMARK 465 PHE A 327 REMARK 465 LEU A 328 REMARK 465 ASN A 329 REMARK 465 HIS A 330 REMARK 465 GLU A 331 REMARK 465 GLU A 332 REMARK 465 LYS A 627 REMARK 465 ASP A 628 REMARK 465 LEU A 629 REMARK 465 GLU A 630 REMARK 465 HIS A 631 REMARK 465 HIS A 632 REMARK 465 HIS A 633 REMARK 465 HIS A 634 REMARK 465 HIS A 635 REMARK 465 ASP B 288 REMARK 465 GLU B 289 REMARK 465 ASN B 290 REMARK 465 ILE B 291 REMARK 465 ASN B 292 REMARK 465 VAL B 293 REMARK 465 ASN B 294 REMARK 465 SER B 295 REMARK 465 GLN B 296 REMARK 465 GLN B 297 REMARK 465 GLN B 298 REMARK 465 VAL B 299 REMARK 465 LEU B 300 REMARK 465 LYS B 301 REMARK 465 ALA B 302 REMARK 465 LEU B 303 REMARK 465 GLN B 304 REMARK 465 LYS B 305 REMARK 465 ASN B 306 REMARK 465 ASN B 307 REMARK 465 VAL B 308 REMARK 465 ARG B 309 REMARK 465 ASP B 310 REMARK 465 ILE B 311 REMARK 465 SER B 312 REMARK 465 ASN B 313 REMARK 465 LYS B 314 REMARK 465 LEU B 315 REMARK 465 ILE B 316 REMARK 465 GLU B 317 REMARK 465 ASN B 318 REMARK 465 THR B 319 REMARK 465 SER B 320 REMARK 465 ASP B 321 REMARK 465 SER B 322 REMARK 465 ASN B 323 REMARK 465 LEU B 324 REMARK 465 LYS B 325 REMARK 465 ASN B 326 REMARK 465 PHE B 327 REMARK 465 LEU B 328 REMARK 465 ASN B 329 REMARK 465 HIS B 330 REMARK 465 GLU B 331 REMARK 465 GLU B 332 REMARK 465 LYS B 627 REMARK 465 ASP B 628 REMARK 465 LEU B 629 REMARK 465 GLU B 630 REMARK 465 HIS B 631 REMARK 465 HIS B 632 REMARK 465 HIS B 633 REMARK 465 HIS B 634 REMARK 465 HIS B 635 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 804 O HOH A 834 1.94 REMARK 500 O LYS A 412 O HOH A 801 2.17 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 LEU A 28 -169.15 -112.21 REMARK 500 ASN A 33 -38.66 -176.11 REMARK 500 ILE A 35 90.74 -63.27 REMARK 500 ASN A 63 -85.37 -75.58 REMARK 500 ASN A 139 76.21 60.63 REMARK 500 ASN A 156 87.83 71.13 REMARK 500 ASP A 215 -8.96 -59.67 REMARK 500 LEU A 282 -71.73 -61.56 REMARK 500 PHE A 349 -71.24 -140.22 REMARK 500 LEU A 371 24.17 -141.03 REMARK 500 ASP A 402 -77.05 -41.73 REMARK 500 THR A 526 -168.26 -107.38 REMARK 500 HIS A 578 -109.97 51.60 REMARK 500 PHE A 589 37.81 -92.87 REMARK 500 LYS B 5 31.83 -95.91 REMARK 500 ASN B 11 32.13 74.81 REMARK 500 ASN B 33 -34.23 -175.36 REMARK 500 LYS B 47 98.06 -62.53 REMARK 500 ASN B 130 105.01 -58.14 REMARK 500 ASN B 139 80.47 63.99 REMARK 500 ASN B 156 96.23 75.49 REMARK 500 PHE B 349 -74.54 -129.63 REMARK 500 LEU B 371 38.75 -140.32 REMARK 500 ASP B 402 -78.64 -38.61 REMARK 500 HIS B 578 -112.43 51.53 REMARK 500 PHE B 589 34.10 -86.52 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 A 701 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 82 OD1 REMARK 620 2 HOH A 804 O 76.3 REMARK 620 3 HOH A 817 O 90.6 73.4 REMARK 620 4 HOH A 834 O 129.7 54.9 66.3 REMARK 620 5 HOH A 837 O 113.4 146.2 74.2 102.6 REMARK 620 6 HOH A 847 O 137.3 104.9 131.3 73.6 89.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 701 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 82 OD1 REMARK 620 2 HOH B 807 O 79.2 REMARK 620 3 HOH B 808 O 97.3 98.8 REMARK 620 4 HOH B 823 O 151.2 73.2 79.2 REMARK 620 5 HOH B 834 O 108.3 87.6 154.4 79.1 REMARK 620 6 HOH B 839 O 118.6 162.1 81.1 89.3 85.3 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 MG A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DKT RELATED DB: PDB DBREF 5DKU A 1 628 UNP Q8ILY1 Q8ILY1_PLAF7 1389 2016 DBREF 5DKU B 1 628 UNP Q8ILY1 Q8ILY1_PLAF7 1389 2016 SEQADV 5DKU ASN A 82 UNP Q8ILY1 ASP 1470 ENGINEERED MUTATION SEQADV 5DKU GLN A 84 UNP Q8ILY1 GLU 1472 ENGINEERED MUTATION SEQADV 5DKU LEU A 629 UNP Q8ILY1 EXPRESSION TAG SEQADV 5DKU GLU A 630 UNP Q8ILY1 EXPRESSION TAG SEQADV 5DKU HIS A 631 UNP Q8ILY1 EXPRESSION TAG SEQADV 5DKU HIS A 632 UNP Q8ILY1 EXPRESSION TAG SEQADV 5DKU HIS A 633 UNP Q8ILY1 EXPRESSION TAG SEQADV 5DKU HIS A 634 UNP Q8ILY1 EXPRESSION TAG SEQADV 5DKU HIS A 635 UNP Q8ILY1 EXPRESSION TAG SEQADV 5DKU ASN B 82 UNP Q8ILY1 ASP 1470 ENGINEERED MUTATION SEQADV 5DKU GLN B 84 UNP Q8ILY1 GLU 1472 ENGINEERED MUTATION SEQADV 5DKU LEU B 629 UNP Q8ILY1 EXPRESSION TAG SEQADV 5DKU GLU B 630 UNP Q8ILY1 EXPRESSION TAG SEQADV 5DKU HIS B 631 UNP Q8ILY1 EXPRESSION TAG SEQADV 5DKU HIS B 632 UNP Q8ILY1 EXPRESSION TAG SEQADV 5DKU HIS B 633 UNP Q8ILY1 EXPRESSION TAG SEQADV 5DKU HIS B 634 UNP Q8ILY1 EXPRESSION TAG SEQADV 5DKU HIS B 635 UNP Q8ILY1 EXPRESSION TAG SEQRES 1 A 635 ASP GLU ILE THR LYS LYS TYR ILE LYS ASP ASN ILE ILE SEQRES 2 A 635 ASN VAL ASP ASP ASN ILE ILE LYS LYS LYS ASP ILE PHE SEQRES 3 A 635 LYS LEU LYS ASN GLU ASN ASN GLU ILE THR GLU CYS ALA SEQRES 4 A 635 PHE GLU TYR PHE GLU SER LYS LYS LYS PHE ASP ASP ASP SEQRES 5 A 635 ILE GLU SER ARG PHE PHE ILE ILE ASN ASP ASN ASN TYR SEQRES 6 A 635 ASN GLU ASN ILE ASN LEU ILE TYR LYS ASP ILE LYS TYR SEQRES 7 A 635 CYS GLY LEU ASN ILE GLN THR THR GLY LEU GLU VAL PHE SEQRES 8 A 635 ASP GLU ASN ILE ARG LEU ILE GLN ILE ALA VAL GLU ASN SEQRES 9 A 635 TYR PRO VAL ILE ILE TYR ASP MET PHE ASN ILE ASN LYS SEQRES 10 A 635 LYS ASP ILE LEU ASP GLY LEU ARG LYS VAL LEU GLU ASN SEQRES 11 A 635 LYS ASN ILE ILE LYS ILE ILE GLN ASN GLY LYS PHE ASP SEQRES 12 A 635 ALA LYS PHE LEU LEU HIS ASN ASN PHE LYS ILE GLU ASN SEQRES 13 A 635 ILE PHE ASP THR TYR ILE ALA SER LYS LEU LEU ASP LYS SEQRES 14 A 635 ASN LYS ASN MET TYR GLY PHE LYS LEU ASN ASN ILE VAL SEQRES 15 A 635 GLU LYS TYR LEU ASN VAL ILE LEU ASP LYS GLN GLN GLN SEQRES 16 A 635 ASN SER VAL TRP ASN ASN SER LEU LEU ASN ASN ASN GLN SEQRES 17 A 635 LEU PHE TYR ALA ALA ARG ASP SER SER CYS LEU LEU LYS SEQRES 18 A 635 LEU TYR LYS LYS LEU LYS GLU GLU ILE LYS LYS GLU ASN SEQRES 19 A 635 LEU HIS ILE VAL ASN ASP ILE GLU ASN LYS CYS ILE LEU SEQRES 20 A 635 PRO ILE CYS ASP MET GLU LEU ASN GLY ILE LYS VAL ASP SEQRES 21 A 635 LEU GLU ASN LEU GLN LYS SER THR ASN GLU ILE LEU ASN SEQRES 22 A 635 GLU LEU ASN ILE GLU LYS ASP ASN LEU LYS LYS LYS LEU SEQRES 23 A 635 LYS ASP GLU ASN ILE ASN VAL ASN SER GLN GLN GLN VAL SEQRES 24 A 635 LEU LYS ALA LEU GLN LYS ASN ASN VAL ARG ASP ILE SER SEQRES 25 A 635 ASN LYS LEU ILE GLU ASN THR SER ASP SER ASN LEU LYS SEQRES 26 A 635 ASN PHE LEU ASN HIS GLU GLU ILE ILE SER LEU ARG ASN SEQRES 27 A 635 TYR ARG ARG LEU TYR LYS LEU TYR SER ALA PHE TYR LEU SEQRES 28 A 635 LYS LEU PRO LEU HIS ILE ASN THR LYS THR ASN LYS ILE SEQRES 29 A 635 HIS THR THR PHE ASN GLN LEU LYS THR PHE SER GLY ARG SEQRES 30 A 635 PHE SER SER GLU LYS PRO ASN LEU GLN GLN ILE PRO ARG SEQRES 31 A 635 GLN LYS ASN ILE ARG GLU ILE PHE ILE PRO ASN ASP ASN SEQRES 32 A 635 ASN ILE PHE ILE ILE ALA ASP PHE LYS GLN ILE GLU LEU SEQRES 33 A 635 LYS ILE ALA ALA GLU ILE THR ASN ASP GLU ILE MET LEU SEQRES 34 A 635 LYS ALA TYR ASN ASN ASN ILE ASP LEU HIS THR LEU THR SEQRES 35 A 635 ALA SER ILE ILE THR LYS LYS ASN ILE PRO ASP ILE ASN SEQRES 36 A 635 LYS GLU ASP ARG HIS ILE ALA LYS ALA ILE ASN PHE GLY SEQRES 37 A 635 LEU ILE TYR GLY MET ASN TYR VAL ASN LEU LYS ASN TYR SEQRES 38 A 635 ALA ASN THR TYR TYR GLY LEU ASN MET SER LEU ASP GLN SEQRES 39 A 635 CYS LEU TYR PHE TYR ASN SER PHE PHE GLU HIS TYR LYS SEQRES 40 A 635 GLY ILE TYR LYS TRP HIS ASN GLN VAL LYS GLN LYS ARG SEQRES 41 A 635 ALA LEU GLN TYR SER THR LEU SER ASN ARG LYS VAL ILE SEQRES 42 A 635 PHE PRO TYR PHE SER PHE THR LYS ALA LEU ASN TYR PRO SEQRES 43 A 635 VAL GLN GLY THR CYS ALA ASP ILE LEU LYS LEU ALA LEU SEQRES 44 A 635 VAL ASP LEU TYR ASP ASN LEU LYS ASP ILE ASN GLY LYS SEQRES 45 A 635 ILE ILE LEU CYS VAL HIS ASP GLU ILE ILE ILE GLU VAL SEQRES 46 A 635 ASN LYS LYS PHE GLN GLU GLU ALA LEU LYS ILE LEU VAL SEQRES 47 A 635 GLN SER MET GLU ASN SER ALA SER TYR PHE LEU LYS LYS SEQRES 48 A 635 VAL LYS CYS GLU VAL SER VAL LYS ILE ALA GLU ASN TRP SEQRES 49 A 635 GLY SER LYS ASP LEU GLU HIS HIS HIS HIS HIS SEQRES 1 B 635 ASP GLU ILE THR LYS LYS TYR ILE LYS ASP ASN ILE ILE SEQRES 2 B 635 ASN VAL ASP ASP ASN ILE ILE LYS LYS LYS ASP ILE PHE SEQRES 3 B 635 LYS LEU LYS ASN GLU ASN ASN GLU ILE THR GLU CYS ALA SEQRES 4 B 635 PHE GLU TYR PHE GLU SER LYS LYS LYS PHE ASP ASP ASP SEQRES 5 B 635 ILE GLU SER ARG PHE PHE ILE ILE ASN ASP ASN ASN TYR SEQRES 6 B 635 ASN GLU ASN ILE ASN LEU ILE TYR LYS ASP ILE LYS TYR SEQRES 7 B 635 CYS GLY LEU ASN ILE GLN THR THR GLY LEU GLU VAL PHE SEQRES 8 B 635 ASP GLU ASN ILE ARG LEU ILE GLN ILE ALA VAL GLU ASN SEQRES 9 B 635 TYR PRO VAL ILE ILE TYR ASP MET PHE ASN ILE ASN LYS SEQRES 10 B 635 LYS ASP ILE LEU ASP GLY LEU ARG LYS VAL LEU GLU ASN SEQRES 11 B 635 LYS ASN ILE ILE LYS ILE ILE GLN ASN GLY LYS PHE ASP SEQRES 12 B 635 ALA LYS PHE LEU LEU HIS ASN ASN PHE LYS ILE GLU ASN SEQRES 13 B 635 ILE PHE ASP THR TYR ILE ALA SER LYS LEU LEU ASP LYS SEQRES 14 B 635 ASN LYS ASN MET TYR GLY PHE LYS LEU ASN ASN ILE VAL SEQRES 15 B 635 GLU LYS TYR LEU ASN VAL ILE LEU ASP LYS GLN GLN GLN SEQRES 16 B 635 ASN SER VAL TRP ASN ASN SER LEU LEU ASN ASN ASN GLN SEQRES 17 B 635 LEU PHE TYR ALA ALA ARG ASP SER SER CYS LEU LEU LYS SEQRES 18 B 635 LEU TYR LYS LYS LEU LYS GLU GLU ILE LYS LYS GLU ASN SEQRES 19 B 635 LEU HIS ILE VAL ASN ASP ILE GLU ASN LYS CYS ILE LEU SEQRES 20 B 635 PRO ILE CYS ASP MET GLU LEU ASN GLY ILE LYS VAL ASP SEQRES 21 B 635 LEU GLU ASN LEU GLN LYS SER THR ASN GLU ILE LEU ASN SEQRES 22 B 635 GLU LEU ASN ILE GLU LYS ASP ASN LEU LYS LYS LYS LEU SEQRES 23 B 635 LYS ASP GLU ASN ILE ASN VAL ASN SER GLN GLN GLN VAL SEQRES 24 B 635 LEU LYS ALA LEU GLN LYS ASN ASN VAL ARG ASP ILE SER SEQRES 25 B 635 ASN LYS LEU ILE GLU ASN THR SER ASP SER ASN LEU LYS SEQRES 26 B 635 ASN PHE LEU ASN HIS GLU GLU ILE ILE SER LEU ARG ASN SEQRES 27 B 635 TYR ARG ARG LEU TYR LYS LEU TYR SER ALA PHE TYR LEU SEQRES 28 B 635 LYS LEU PRO LEU HIS ILE ASN THR LYS THR ASN LYS ILE SEQRES 29 B 635 HIS THR THR PHE ASN GLN LEU LYS THR PHE SER GLY ARG SEQRES 30 B 635 PHE SER SER GLU LYS PRO ASN LEU GLN GLN ILE PRO ARG SEQRES 31 B 635 GLN LYS ASN ILE ARG GLU ILE PHE ILE PRO ASN ASP ASN SEQRES 32 B 635 ASN ILE PHE ILE ILE ALA ASP PHE LYS GLN ILE GLU LEU SEQRES 33 B 635 LYS ILE ALA ALA GLU ILE THR ASN ASP GLU ILE MET LEU SEQRES 34 B 635 LYS ALA TYR ASN ASN ASN ILE ASP LEU HIS THR LEU THR SEQRES 35 B 635 ALA SER ILE ILE THR LYS LYS ASN ILE PRO ASP ILE ASN SEQRES 36 B 635 LYS GLU ASP ARG HIS ILE ALA LYS ALA ILE ASN PHE GLY SEQRES 37 B 635 LEU ILE TYR GLY MET ASN TYR VAL ASN LEU LYS ASN TYR SEQRES 38 B 635 ALA ASN THR TYR TYR GLY LEU ASN MET SER LEU ASP GLN SEQRES 39 B 635 CYS LEU TYR PHE TYR ASN SER PHE PHE GLU HIS TYR LYS SEQRES 40 B 635 GLY ILE TYR LYS TRP HIS ASN GLN VAL LYS GLN LYS ARG SEQRES 41 B 635 ALA LEU GLN TYR SER THR LEU SER ASN ARG LYS VAL ILE SEQRES 42 B 635 PHE PRO TYR PHE SER PHE THR LYS ALA LEU ASN TYR PRO SEQRES 43 B 635 VAL GLN GLY THR CYS ALA ASP ILE LEU LYS LEU ALA LEU SEQRES 44 B 635 VAL ASP LEU TYR ASP ASN LEU LYS ASP ILE ASN GLY LYS SEQRES 45 B 635 ILE ILE LEU CYS VAL HIS ASP GLU ILE ILE ILE GLU VAL SEQRES 46 B 635 ASN LYS LYS PHE GLN GLU GLU ALA LEU LYS ILE LEU VAL SEQRES 47 B 635 GLN SER MET GLU ASN SER ALA SER TYR PHE LEU LYS LYS SEQRES 48 B 635 VAL LYS CYS GLU VAL SER VAL LYS ILE ALA GLU ASN TRP SEQRES 49 B 635 GLY SER LYS ASP LEU GLU HIS HIS HIS HIS HIS HET MG A 701 1 HET MG B 701 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *93(H2 O) HELIX 1 AA1 ILE A 3 ASP A 10 5 8 HELIX 2 AA2 ASN A 66 TYR A 73 5 8 HELIX 3 AA3 GLU A 89 GLU A 93 5 5 HELIX 4 AA4 PHE A 113 ILE A 115 5 3 HELIX 5 AA5 LYS A 117 ASN A 130 1 14 HELIX 6 AA6 ASN A 139 ASN A 150 1 12 HELIX 7 AA7 THR A 160 LYS A 169 1 10 HELIX 8 AA8 LYS A 177 LEU A 186 1 10 HELIX 9 AA9 LYS A 192 SER A 197 5 6 HELIX 10 AB1 ASN A 206 GLU A 233 1 28 HELIX 11 AB2 LEU A 235 GLY A 256 1 22 HELIX 12 AB3 ASP A 260 LYS A 283 1 24 HELIX 13 AB4 ILE A 334 ALA A 348 1 15 HELIX 14 AB5 LYS A 352 ILE A 357 1 6 HELIX 15 AB6 ASN A 384 ILE A 388 5 5 HELIX 16 AB7 GLN A 391 GLU A 396 1 6 HELIX 17 AB8 GLN A 413 ASN A 424 1 12 HELIX 18 AB9 ASP A 425 ASN A 434 1 10 HELIX 19 AC1 ASP A 437 LYS A 448 1 12 HELIX 20 AC2 ASN A 450 ILE A 454 5 5 HELIX 21 AC3 ASN A 455 ILE A 470 1 16 HELIX 22 AC4 ASN A 474 TYR A 486 1 13 HELIX 23 AC5 SER A 491 TYR A 506 1 16 HELIX 24 AC6 TYR A 506 ARG A 520 1 15 HELIX 25 AC7 SER A 538 LEU A 566 1 29 HELIX 26 AC8 PHE A 589 LEU A 609 1 21 HELIX 27 AC9 TYR B 7 ASP B 10 5 4 HELIX 28 AD1 ASN B 66 TYR B 73 5 8 HELIX 29 AD2 GLU B 89 GLU B 93 5 5 HELIX 30 AD3 PHE B 113 ILE B 115 5 3 HELIX 31 AD4 LYS B 117 ASN B 130 1 14 HELIX 32 AD5 ASN B 139 ASN B 150 1 12 HELIX 33 AD6 THR B 160 LYS B 169 1 10 HELIX 34 AD7 LYS B 177 LEU B 186 1 10 HELIX 35 AD8 LYS B 192 SER B 197 5 6 HELIX 36 AD9 ASN B 206 GLU B 233 1 28 HELIX 37 AE1 LEU B 235 GLY B 256 1 22 HELIX 38 AE2 ASP B 260 LEU B 286 1 27 HELIX 39 AE3 ILE B 334 ALA B 348 1 15 HELIX 40 AE4 LYS B 352 ILE B 357 5 6 HELIX 41 AE5 ASN B 384 ILE B 388 5 5 HELIX 42 AE6 GLN B 391 GLU B 396 1 6 HELIX 43 AE7 GLN B 413 ASN B 424 1 12 HELIX 44 AE8 ASP B 425 ASN B 434 1 10 HELIX 45 AE9 ASP B 437 LYS B 448 1 12 HELIX 46 AF1 ASN B 450 ILE B 454 5 5 HELIX 47 AF2 ASN B 455 TYR B 471 1 17 HELIX 48 AF3 ASN B 474 TYR B 486 1 13 HELIX 49 AF4 SER B 491 TYR B 506 1 16 HELIX 50 AF5 TYR B 506 ARG B 520 1 15 HELIX 51 AF6 SER B 538 LEU B 566 1 29 HELIX 52 AF7 PHE B 589 LEU B 609 1 21 SHEET 1 AA1 2 ILE A 12 ILE A 13 0 SHEET 2 AA1 2 LEU A 204 ASN A 205 1 O LEU A 204 N ILE A 13 SHEET 1 AA2 2 ILE A 19 LYS A 27 0 SHEET 2 AA2 2 GLU A 37 SER A 45 -1 O PHE A 40 N ASP A 24 SHEET 1 AA3 6 PHE A 57 ILE A 60 0 SHEET 2 AA3 6 VAL A 107 ASP A 111 1 O ILE A 109 N ILE A 60 SHEET 3 AA3 6 ILE A 95 ALA A 101 -1 N ILE A 98 O TYR A 110 SHEET 4 AA3 6 TYR A 78 THR A 85 -1 N ASN A 82 O GLN A 99 SHEET 5 AA3 6 ILE A 134 ILE A 137 1 O ILE A 136 N CYS A 79 SHEET 6 AA3 6 ILE A 157 ASP A 159 1 O PHE A 158 N ILE A 137 SHEET 1 AA4 3 LYS A 363 ILE A 364 0 SHEET 2 AA4 3 ILE A 257 VAL A 259 -1 N ILE A 257 O ILE A 364 SHEET 3 AA4 3 PHE A 398 ILE A 399 -1 O ILE A 399 N LYS A 258 SHEET 1 AA5 2 THR A 367 ASN A 369 0 SHEET 2 AA5 2 SER A 379 GLU A 381 -1 O SER A 379 N ASN A 369 SHEET 1 AA6 4 LYS A 572 VAL A 577 0 SHEET 2 AA6 4 GLU A 580 ASN A 586 -1 O GLU A 584 N LYS A 572 SHEET 3 AA6 4 ASN A 404 PHE A 411 -1 N ILE A 407 O ILE A 583 SHEET 4 AA6 4 VAL A 616 ALA A 621 -1 O LYS A 619 N ILE A 408 SHEET 1 AA7 2 GLN A 523 SER A 525 0 SHEET 2 AA7 2 LYS A 531 ILE A 533 -1 O VAL A 532 N TYR A 524 SHEET 1 AA8 2 ILE B 12 ILE B 13 0 SHEET 2 AA8 2 LEU B 204 ASN B 205 1 O LEU B 204 N ILE B 13 SHEET 1 AA9 2 ILE B 19 LYS B 27 0 SHEET 2 AA9 2 GLU B 37 SER B 45 -1 O CYS B 38 N PHE B 26 SHEET 1 AB1 6 PHE B 57 ILE B 60 0 SHEET 2 AB1 6 VAL B 107 ASP B 111 1 O VAL B 107 N PHE B 58 SHEET 3 AB1 6 ILE B 95 ALA B 101 -1 N ILE B 98 O TYR B 110 SHEET 4 AB1 6 TYR B 78 THR B 85 -1 N ASN B 82 O GLN B 99 SHEET 5 AB1 6 ILE B 134 ILE B 137 1 O ILE B 136 N LEU B 81 SHEET 6 AB1 6 ILE B 157 ASP B 159 1 O PHE B 158 N LYS B 135 SHEET 1 AB2 3 LYS B 363 ILE B 364 0 SHEET 2 AB2 3 ILE B 257 VAL B 259 -1 N ILE B 257 O ILE B 364 SHEET 3 AB2 3 PHE B 398 ILE B 399 -1 O ILE B 399 N LYS B 258 SHEET 1 AB3 2 THR B 367 ASN B 369 0 SHEET 2 AB3 2 SER B 379 GLU B 381 -1 O SER B 379 N ASN B 369 SHEET 1 AB4 4 LYS B 572 VAL B 577 0 SHEET 2 AB4 4 GLU B 580 ASN B 586 -1 O GLU B 584 N LYS B 572 SHEET 3 AB4 4 ASN B 404 PHE B 411 -1 N ILE B 407 O ILE B 583 SHEET 4 AB4 4 VAL B 616 ALA B 621 -1 O LYS B 619 N ILE B 408 SHEET 1 AB5 2 GLN B 523 SER B 525 0 SHEET 2 AB5 2 LYS B 531 ILE B 533 -1 O VAL B 532 N TYR B 524 LINK OD1 ASN A 82 MG MG A 701 1555 1555 2.10 LINK MG MG A 701 O HOH A 804 1555 1555 2.10 LINK MG MG A 701 O HOH A 817 1555 1555 2.10 LINK MG MG A 701 O HOH A 834 1555 1555 2.10 LINK MG MG A 701 O HOH A 837 1555 1555 2.10 LINK MG MG A 701 O HOH A 847 1555 1555 2.10 LINK OD1 ASN B 82 MG MG B 701 1555 1555 2.10 LINK MG MG B 701 O HOH B 807 1555 1555 2.10 LINK MG MG B 701 O HOH B 808 1555 1555 2.10 LINK MG MG B 701 O HOH B 823 1555 1555 2.10 LINK MG MG B 701 O HOH B 834 1555 1555 2.10 LINK MG MG B 701 O HOH B 839 1555 1555 2.10 CISPEP 1 LYS A 382 PRO A 383 0 -2.46 CISPEP 2 LYS B 382 PRO B 383 0 -2.91 SITE 1 AC1 6 ASN A 82 HOH A 804 HOH A 817 HOH A 834 SITE 2 AC1 6 HOH A 837 HOH A 847 SITE 1 AC2 6 ASN B 82 HOH B 807 HOH B 808 HOH B 823 SITE 2 AC2 6 HOH B 834 HOH B 839 CRYST1 146.382 146.382 165.671 90.00 90.00 120.00 P 65 12 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 0.006831 0.003944 0.000000 0.00000 SCALE2 0.000000 0.007888 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006036 0.00000