HEADER REPLICATION 18-JUN-18 6DU0 TITLE CRYSTAL STRUCTURE OF EUKARYOTIC DNA PRIMASE LARGE SUBUNIT IRON-SULFUR TITLE 2 CLUSTER DOMAIN Y395L MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA PRIMASE LARGE SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DNA POLYMERASE ALPHA:PRIMASE COMPLEX P58 SUBUNIT,POL ALPHA- COMPND 5 PRIMASE COMPLEX P58 SUBUNIT,DNA PRIMASE 58 KDA SUBUNIT; COMPND 6 EC: 2.7.7.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: PRI2, YKL045W, YKL258; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA PRIMASE, P58, IRON-SULFUR CLUSTER, REPLICATION, REGULATORY KEYWDS 2 SUBUNIT EXPDTA X-RAY DIFFRACTION AUTHOR L.E.SALAY,W.J.CHAZIN REVDAT 5 11-OCT-23 6DU0 1 REMARK REVDAT 4 01-JAN-20 6DU0 1 REMARK REVDAT 3 09-JAN-19 6DU0 1 JRNL REVDAT 2 26-DEC-18 6DU0 1 JRNL REVDAT 1 12-DEC-18 6DU0 0 JRNL AUTH E.O'BRIEN,L.E.SALAY,E.A.EPUM,K.L.FRIEDMAN,W.J.CHAZIN, JRNL AUTH 2 J.K.BARTON JRNL TITL YEAST REQUIRE REDOX SWITCHING IN DNA PRIMASE. JRNL REF PROC. NATL. ACAD. SCI. V. 115 13186 2018 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 30541886 JRNL DOI 10.1073/PNAS.1810715115 REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 15173 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.276 REMARK 3 R VALUE (WORKING SET) : 0.273 REMARK 3 FREE R VALUE : 0.324 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 847 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1010 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.5110 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.4710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1431 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.21000 REMARK 3 B22 (A**2) : -5.46000 REMARK 3 B33 (A**2) : -5.75000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.204 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.189 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.320 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.348 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1502 ; 0.010 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 1300 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2028 ; 1.156 ; 1.684 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3024 ; 1.313 ; 1.674 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 177 ; 6.343 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 79 ;35.696 ;20.759 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 244 ;16.152 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;20.491 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 196 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1650 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 298 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6DU0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000235231. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29372 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 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: PHASER 2.7.17 REMARK 200 STARTING MODEL: 6DTZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS 8.5, 40-60% MPD, PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 19.23100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.08750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.41500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.08750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.23100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.41500 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 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 GLY A 312 REMARK 465 PRO A 313 REMARK 465 GLY A 314 REMARK 465 SER A 315 REMARK 465 ASP A 316 REMARK 465 GLY A 407 REMARK 465 ASN A 408 REMARK 465 ASN A 483 REMARK 465 SER A 484 REMARK 465 ALA A 485 REMARK 465 SER A 486 REMARK 465 ALA A 487 REMARK 465 ASP A 488 REMARK 465 LEU A 489 REMARK 465 GLU A 490 REMARK 465 ILE A 491 REMARK 465 GLY A 492 REMARK 465 GLU A 493 REMARK 465 GLN A 494 REMARK 465 THR A 495 REMARK 465 HIS A 496 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 ASP A 317 CG OD1 OD2 REMARK 470 GLU A 318 CG CD OE1 OE2 REMARK 470 GLU A 342 CG CD OE1 OE2 REMARK 470 GLU A 389 CG CD OE1 OE2 REMARK 470 LYS A 393 CG CD CE NZ REMARK 470 ARG A 409 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 413 CG CD CE NZ REMARK 470 ARG A 428 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 442 CG CD OE1 OE2 REMARK 470 GLN A 455 CG CD OE1 NE2 REMARK 470 GLN A 466 CG CD OE1 NE2 REMARK 470 LYS A 467 CG CD CE NZ REMARK 470 GLU A 479 CG CD OE1 OE2 REMARK 470 GLU A 505 CG CD OE1 OE2 REMARK 470 GLN A 509 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 OD1 ASP A 416 OG1 THR A 419 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 ARG A 382 153.93 -47.17 REMARK 500 LYS A 452 47.26 70.63 REMARK 500 GLU A 469 66.46 -109.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 396 0.08 SIDE CHAIN 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 SF4 A 602 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 336 SG REMARK 620 2 SF4 A 602 S1 124.6 REMARK 620 3 SF4 A 602 S2 117.0 91.6 REMARK 620 4 SF4 A 602 S4 127.6 92.4 94.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 602 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 417 SG REMARK 620 2 SF4 A 602 S1 155.2 REMARK 620 3 SF4 A 602 S2 105.5 88.2 REMARK 620 4 SF4 A 602 S3 114.7 85.9 88.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 602 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 434 SG REMARK 620 2 SF4 A 602 S1 116.7 REMARK 620 3 SF4 A 602 S3 139.5 87.9 REMARK 620 4 SF4 A 602 S4 118.0 93.1 90.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 602 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 474 SG REMARK 620 2 SF4 A 602 S2 140.7 REMARK 620 3 SF4 A 602 S3 119.5 87.4 REMARK 620 4 SF4 A 602 S4 111.3 94.8 91.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6DI2 RELATED DB: PDB REMARK 900 RELATED ID: 6DI6 RELATED DB: PDB REMARK 900 RELATED ID: 6DTV RELATED DB: PDB REMARK 900 RELATED ID: 6DTZ RELATED DB: PDB DBREF 6DU0 A 316 512 UNP P20457 PRI2_YEAST 316 512 SEQADV 6DU0 GLY A 312 UNP P20457 EXPRESSION TAG SEQADV 6DU0 PRO A 313 UNP P20457 EXPRESSION TAG SEQADV 6DU0 GLY A 314 UNP P20457 EXPRESSION TAG SEQADV 6DU0 SER A 315 UNP P20457 EXPRESSION TAG SEQADV 6DU0 LEU A 395 UNP P20457 TYR 395 ENGINEERED MUTATION SEQRES 1 A 201 GLY PRO GLY SER ASP ASP GLU ILE ASN ALA GLN SER VAL SEQRES 2 A 201 TRP SER GLU GLU ILE SER SER ASN TYR PRO LEU CYS ILE SEQRES 3 A 201 LYS ASN LEU MET GLU GLY LEU LYS LYS ASN HIS HIS LEU SEQRES 4 A 201 ARG TYR TYR GLY ARG GLN GLN LEU SER LEU PHE LEU LYS SEQRES 5 A 201 GLY ILE GLY LEU SER ALA ASP GLU ALA LEU LYS PHE TRP SEQRES 6 A 201 SER GLU ALA PHE THR ARG ASN GLY ASN MET THR MET GLU SEQRES 7 A 201 LYS PHE ASN LYS GLU LEU ARG TYR SER PHE ARG HIS ASN SEQRES 8 A 201 TYR GLY LEU GLU GLY ASN ARG ILE ASN TYR LYS PRO TRP SEQRES 9 A 201 ASP CYS HIS THR ILE LEU SER LYS PRO ARG PRO GLY ARG SEQRES 10 A 201 GLY ASP TYR HIS GLY CYS PRO PHE ARG ASP TRP SER HIS SEQRES 11 A 201 GLU ARG LEU SER ALA GLU LEU ARG SER MET LYS LEU THR SEQRES 12 A 201 GLN ALA GLN ILE ILE SER VAL LEU ASP SER CYS GLN LYS SEQRES 13 A 201 GLY GLU TYR THR ILE ALA CYS THR LYS VAL PHE GLU MET SEQRES 14 A 201 THR HIS ASN SER ALA SER ALA ASP LEU GLU ILE GLY GLU SEQRES 15 A 201 GLN THR HIS ILE ALA HIS PRO ASN LEU TYR PHE GLU ARG SEQRES 16 A 201 SER ARG GLN LEU GLN LYS HET GOL A 601 6 HET SF4 A 602 8 HET MPD A 603 8 HET MPD A 604 8 HETNAM GOL GLYCEROL HETNAM SF4 IRON/SULFUR CLUSTER HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 SF4 FE4 S4 FORMUL 4 MPD 2(C6 H14 O2) FORMUL 6 HOH *13(H2 O) HELIX 1 AA1 GLN A 322 TRP A 325 5 4 HELIX 2 AA2 SER A 326 SER A 331 1 6 HELIX 3 AA3 PRO A 334 HIS A 348 1 15 HELIX 4 AA4 ARG A 351 ILE A 365 1 15 HELIX 5 AA5 SER A 368 ARG A 382 1 15 HELIX 6 AA6 ASN A 383 ASN A 385 5 3 HELIX 7 AA7 THR A 387 LEU A 395 1 9 HELIX 8 AA8 LEU A 395 TYR A 403 1 9 HELIX 9 AA9 ASP A 416 LYS A 423 1 8 HELIX 10 AB1 CYS A 434 TRP A 439 1 6 HELIX 11 AB2 SER A 440 SER A 450 1 11 HELIX 12 AB3 THR A 454 LYS A 467 1 14 HELIX 13 AB4 GLU A 469 THR A 481 1 13 HELIX 14 AB5 HIS A 499 LYS A 512 1 14 LINK SG CYS A 336 FE3 SF4 A 602 1555 1555 2.28 LINK SG CYS A 417 FE4 SF4 A 602 1555 1555 2.36 LINK SG CYS A 434 FE2 SF4 A 602 1555 1555 2.28 LINK SG CYS A 474 FE1 SF4 A 602 1555 1555 2.24 SITE 1 AC1 1 ILE A 497 SITE 1 AC2 6 CYS A 336 CYS A 417 CYS A 434 PHE A 436 SITE 2 AC2 6 CYS A 474 MPD A 603 SITE 1 AC3 9 CYS A 417 THR A 471 THR A 475 PHE A 478 SITE 2 AC3 9 ILE A 497 ALA A 498 HIS A 499 ARG A 506 SITE 3 AC3 9 SF4 A 602 CRYST1 38.462 50.830 90.175 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 0.026000 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019673 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011090 0.00000