HEADER HYDROLASE/DNA 13-JAN-24 8VNS TITLE HOMING ENDONUCLEASE I-PPOI-DNA COMPLEX:REACTION AT PH6.0 (K+ MES) WITH TITLE 2 200 MM MN2+ FOR 600S COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3'); COMPND 3 CHAIN: C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3'); COMPND 7 CHAIN: c, d; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: INTRON-ENCODED ENDONUCLEASE I-PPOI; COMPND 11 CHAIN: A, B; COMPND 12 SYNONYM: I-PPO; COMPND 13 EC: 3.1.-.-; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: PHYSARUM POLYCEPHALUM; SOURCE 11 ORGANISM_TAXID: 5791; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS INTRON ENCODED HOMING ENDONUCLEASE I-PPOI, HYDROLASE, HYDROLASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.CHANG,Y.GAO REVDAT 2 17-JUL-24 8VNS 1 REMARK REVDAT 1 10-JUL-24 8VNS 0 JRNL AUTH C.CHANG,Y.GAO JRNL TITL HOMING ENDONUCLEASE I-PPOI-DNA COMPLEX:REACTION WITH 500 UM JRNL TITL 2 MG2+ FOR 160S JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 39240 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1910 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 48.3900 - 5.0900 0.99 2803 153 0.1755 0.2186 REMARK 3 2 5.0800 - 4.0400 1.00 2714 126 0.1615 0.1877 REMARK 3 3 4.0400 - 3.5300 1.00 2720 130 0.2013 0.1906 REMARK 3 4 3.5300 - 3.2000 1.00 2673 149 0.2323 0.2558 REMARK 3 5 3.2000 - 2.9800 1.00 2687 131 0.2721 0.2937 REMARK 3 6 2.9700 - 2.8000 1.00 2657 121 0.2809 0.2953 REMARK 3 7 2.8000 - 2.6600 1.00 2695 125 0.2710 0.3204 REMARK 3 8 2.6600 - 2.5400 1.00 2652 129 0.2848 0.3203 REMARK 3 9 2.5400 - 2.4500 1.00 2651 153 0.2630 0.2891 REMARK 3 10 2.4500 - 2.3600 1.00 2600 157 0.2629 0.3183 REMARK 3 11 2.3600 - 2.2900 1.00 2643 150 0.2478 0.2708 REMARK 3 12 2.2900 - 2.2200 1.00 2648 123 0.2499 0.3888 REMARK 3 13 2.2200 - 2.1600 1.00 2639 151 0.2490 0.2993 REMARK 3 14 2.1600 - 2.1100 0.96 2548 112 0.2668 0.3513 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 27.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.010 3647 REMARK 3 ANGLE : 1.144 5185 REMARK 3 CHIRALITY : 0.077 563 REMARK 3 PLANARITY : 0.007 516 REMARK 3 DIHEDRAL : 20.193 1363 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 8VNS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1000280584. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9765 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75423 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 200 RESOLUTION RANGE LOW (A) : 48.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54900 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM MALONATE, PEG 3350, 0.1 M REMARK 280 MES, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 28.24767 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 56.49533 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 56.49533 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 28.24767 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, c, D, d, A, 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DA C 404 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG c 416 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA d 521 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 70 17.15 56.89 REMARK 500 SER A 159 41.48 -150.15 REMARK 500 GLN B 270 18.68 56.99 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 MN C 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA C 413 O3' REMARK 620 2 DA C 413 O3' 4.7 REMARK 620 3 DG c 414 P 40.2 44.9 REMARK 620 4 DG c 414 OP2 76.0 80.7 36.5 REMARK 620 5 HOH c 503 O 93.3 93.1 95.0 86.2 REMARK 620 6 ASN B 319 OD1 103.6 103.2 101.6 103.2 162.2 REMARK 620 7 HOH B 501 O 103.7 99.0 143.4 178.8 92.7 78.0 REMARK 620 8 HOH B 506 O 173.6 174.0 136.7 100.3 81.1 82.3 79.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 502 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA C 413 O3' REMARK 620 2 DA C 413 O3' 4.7 REMARK 620 3 DG c 414 OP2 76.7 81.3 REMARK 620 4 HOH c 503 O 93.2 92.9 87.4 REMARK 620 5 ASN B 319 OD1 103.0 102.6 104.4 161.7 REMARK 620 6 HOH B 501 O 101.9 97.3 178.2 91.6 77.0 REMARK 620 7 HOH B 506 O 174.6 173.2 102.1 81.5 82.4 79.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 601 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA D 513 O3' REMARK 620 2 DA D 513 O3' 4.3 REMARK 620 3 HOH D 705 O 92.4 92.2 REMARK 620 4 DG d 514 P 39.9 44.2 100.2 REMARK 620 5 DG d 514 OP1 75.0 79.3 96.3 35.6 REMARK 620 6 ASN A 119 OD1 100.8 100.2 163.2 96.6 97.1 REMARK 620 7 HOH A 701 O 99.4 95.1 82.3 139.1 174.3 85.3 REMARK 620 8 HOH A 702 O 170.7 175.0 87.1 131.1 95.8 81.5 89.7 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA D 602 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA D 513 O3' REMARK 620 2 DA D 513 O3' 4.3 REMARK 620 3 HOH D 705 O 92.6 92.4 REMARK 620 4 DG d 514 OP1 74.8 79.1 95.7 REMARK 620 5 ASN A 119 OD1 101.2 100.6 163.5 96.6 REMARK 620 6 HOH A 701 O 100.4 96.0 82.8 174.9 85.9 REMARK 620 7 HOH A 702 O 169.6 173.9 86.8 94.9 81.3 89.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 41 SG REMARK 620 2 CYS A 100 SG 109.7 REMARK 620 3 CYS A 105 SG 109.8 113.5 REMARK 620 4 HIS A 110 ND1 108.9 104.6 110.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 125 SG REMARK 620 2 CYS A 132 SG 107.2 REMARK 620 3 HIS A 134 ND1 112.7 105.8 REMARK 620 4 CYS A 138 SG 108.3 117.0 106.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 241 SG REMARK 620 2 CYS B 300 SG 113.0 REMARK 620 3 CYS B 305 SG 108.2 113.8 REMARK 620 4 HIS B 310 ND1 107.9 107.1 106.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 325 SG REMARK 620 2 CYS B 332 SG 107.1 REMARK 620 3 HIS B 334 ND1 116.0 106.2 REMARK 620 4 CYS B 338 SG 109.9 116.4 101.5 REMARK 620 N 1 2 3 DBREF 8VNS C 401 413 PDB 8VNS 8VNS 401 413 DBREF 8VNS c 414 421 PDB 8VNS 8VNS 414 421 DBREF 8VNS D 501 513 PDB 8VNS 8VNS 501 513 DBREF 8VNS d 514 521 PDB 8VNS 8VNS 514 521 DBREF 8VNS A 2 163 UNP Q94702 PPO1_PHYPO 2 163 DBREF 8VNS B 202 363 UNP Q94702 PPO1_PHYPO 2 163 SEQRES 1 C 13 DT DT DG DA DC DT DC DT DC DT DT DA DA SEQRES 1 c 8 DG DA DG DA DG DT DC DA SEQRES 1 D 13 DT DT DG DA DC DT DC DT DC DT DT DA DA SEQRES 1 d 8 DG DA DG DA DG DT DC DA SEQRES 1 A 162 ALA LEU THR ASN ALA GLN ILE LEU ALA VAL ILE ASP SER SEQRES 2 A 162 TRP GLU GLU THR VAL GLY GLN PHE PRO VAL ILE THR HIS SEQRES 3 A 162 HIS VAL PRO LEU GLY GLY GLY LEU GLN GLY THR LEU HIS SEQRES 4 A 162 CYS TYR GLU ILE PRO LEU ALA ALA PRO TYR GLY VAL GLY SEQRES 5 A 162 PHE ALA LYS ASN GLY PRO THR ARG TRP GLN TYR LYS ARG SEQRES 6 A 162 THR ILE ASN GLN VAL VAL HIS ARG TRP GLY SER HIS THR SEQRES 7 A 162 VAL PRO PHE LEU LEU GLU PRO ASP ASN ILE ASN GLY LYS SEQRES 8 A 162 THR CYS THR ALA SER HIS LEU CYS HIS ASN THR ARG CYS SEQRES 9 A 162 HIS ASN PRO LEU HIS LEU CYS TRP GLU SER LEU ASP ASP SEQRES 10 A 162 ASN LYS GLY ARG ASN TRP CYS PRO GLY PRO ASN GLY GLY SEQRES 11 A 162 CYS VAL HIS ALA VAL VAL CYS LEU ARG GLN GLY PRO LEU SEQRES 12 A 162 TYR GLY PRO GLY ALA THR VAL ALA GLY PRO GLN GLN ARG SEQRES 13 A 162 GLY SER HIS PHE VAL VAL SEQRES 1 B 162 ALA LEU THR ASN ALA GLN ILE LEU ALA VAL ILE ASP SER SEQRES 2 B 162 TRP GLU GLU THR VAL GLY GLN PHE PRO VAL ILE THR HIS SEQRES 3 B 162 HIS VAL PRO LEU GLY GLY GLY LEU GLN GLY THR LEU HIS SEQRES 4 B 162 CYS TYR GLU ILE PRO LEU ALA ALA PRO TYR GLY VAL GLY SEQRES 5 B 162 PHE ALA LYS ASN GLY PRO THR ARG TRP GLN TYR LYS ARG SEQRES 6 B 162 THR ILE ASN GLN VAL VAL HIS ARG TRP GLY SER HIS THR SEQRES 7 B 162 VAL PRO PHE LEU LEU GLU PRO ASP ASN ILE ASN GLY LYS SEQRES 8 B 162 THR CYS THR ALA SER HIS LEU CYS HIS ASN THR ARG CYS SEQRES 9 B 162 HIS ASN PRO LEU HIS LEU CYS TRP GLU SER LEU ASP ASP SEQRES 10 B 162 ASN LYS GLY ARG ASN TRP CYS PRO GLY PRO ASN GLY GLY SEQRES 11 B 162 CYS VAL HIS ALA VAL VAL CYS LEU ARG GLN GLY PRO LEU SEQRES 12 B 162 TYR GLY PRO GLY ALA THR VAL ALA GLY PRO GLN GLN ARG SEQRES 13 B 162 GLY SER HIS PHE VAL VAL HET MN C 501 1 HET NA C 502 1 HET MN D 601 1 HET NA D 602 1 HET ZN A 601 1 HET ZN A 602 1 HET ZN B 401 1 HET ZN B 402 1 HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM ZN ZINC ION FORMUL 7 MN 2(MN 2+) FORMUL 8 NA 2(NA 1+) FORMUL 11 ZN 4(ZN 2+) FORMUL 15 HOH *46(H2 O) HELIX 1 AA1 THR A 4 GLY A 20 1 17 HELIX 2 AA2 THR A 79 LEU A 83 5 5 HELIX 3 AA3 ASN A 107 LEU A 109 5 3 HELIX 4 AA4 SER A 115 ARG A 122 1 8 HELIX 5 AA5 ASN A 123 CYS A 125 5 3 HELIX 6 AA6 THR B 204 GLY B 220 1 17 HELIX 7 AA7 THR B 279 LEU B 283 5 5 HELIX 8 AA8 ASN B 307 LEU B 309 5 3 HELIX 9 AA9 LEU B 316 ARG B 322 1 7 HELIX 10 AB1 ASN B 323 CYS B 325 5 3 SHEET 1 AA1 2 VAL A 24 GLY A 32 0 SHEET 2 AA1 2 LEU A 35 TYR A 42 -1 O CYS A 41 N ILE A 25 SHEET 1 AA2 3 PHE A 54 GLY A 58 0 SHEET 2 AA2 3 ARG A 61 ILE A 68 -1 O GLN A 63 N ALA A 55 SHEET 3 AA2 3 VAL A 71 GLY A 76 -1 O VAL A 71 N ILE A 68 SHEET 1 AA3 2 ASN A 88 ILE A 89 0 SHEET 2 AA3 2 LYS A 92 THR A 93 -1 O LYS A 92 N ILE A 89 SHEET 1 AA4 2 THR A 95 HIS A 98 0 SHEET 2 AA4 2 LEU A 111 GLU A 114 -1 O GLU A 114 N THR A 95 SHEET 1 AA5 2 VAL B 224 GLY B 232 0 SHEET 2 AA5 2 LEU B 235 TYR B 242 -1 O CYS B 241 N ILE B 225 SHEET 1 AA6 3 PHE B 254 GLY B 258 0 SHEET 2 AA6 3 ARG B 261 ILE B 268 -1 O GLN B 263 N ALA B 255 SHEET 3 AA6 3 VAL B 271 GLY B 276 -1 O VAL B 271 N ILE B 268 SHEET 1 AA7 3 ASN B 288 ILE B 289 0 SHEET 2 AA7 3 LYS B 292 HIS B 298 -1 O LYS B 292 N ILE B 289 SHEET 3 AA7 3 LEU B 311 SER B 315 -1 O GLU B 314 N THR B 295 LINK O3'A DA C 413 MN MN C 501 1555 1555 2.10 LINK O3'B DA C 413 MN MN C 501 1555 1555 2.12 LINK O3'A DA C 413 NA NA C 502 1555 1555 2.11 LINK O3'B DA C 413 NA NA C 502 1555 1555 2.13 LINK MN MN C 501 P A DG c 414 1555 1555 2.52 LINK MN MN C 501 OP2A DG c 414 1555 1555 1.98 LINK MN MN C 501 O HOH c 503 1555 1555 2.04 LINK MN MN C 501 OD1 ASN B 319 1555 1555 2.06 LINK MN MN C 501 O HOH B 501 1555 1555 1.91 LINK MN MN C 501 O HOH B 506 1555 1555 2.04 LINK NA NA C 502 OP2A DG c 414 1555 1555 1.94 LINK NA NA C 502 O HOH c 503 1555 1555 2.04 LINK NA NA C 502 OD1 ASN B 319 1555 1555 2.06 LINK NA NA C 502 O HOH B 501 1555 1555 1.95 LINK NA NA C 502 O HOH B 506 1555 1555 2.03 LINK O3'A DA D 513 MN MN D 601 1555 1555 2.05 LINK O3'B DA D 513 MN MN D 601 1555 1555 2.07 LINK O3'A DA D 513 NA NA D 602 1555 1555 2.04 LINK O3'B DA D 513 NA NA D 602 1555 1555 2.06 LINK MN MN D 601 O HOH D 705 1555 1555 2.09 LINK MN MN D 601 P A DG d 514 1555 1555 2.55 LINK MN MN D 601 OP1A DG d 514 1555 1555 2.09 LINK MN MN D 601 OD1 ASN A 119 1555 1555 2.06 LINK MN MN D 601 O HOH A 701 1555 1555 2.21 LINK MN MN D 601 O HOH A 702 1555 1555 2.01 LINK NA NA D 602 O HOH D 705 1555 1555 2.09 LINK NA NA D 602 OP1A DG d 514 1555 1555 2.11 LINK NA NA D 602 OD1 ASN A 119 1555 1555 2.06 LINK NA NA D 602 O HOH A 701 1555 1555 2.19 LINK NA NA D 602 O HOH A 702 1555 1555 2.02 LINK SG CYS A 41 ZN ZN A 602 1555 1555 2.34 LINK SG CYS A 100 ZN ZN A 602 1555 1555 2.34 LINK SG CYS A 105 ZN ZN A 602 1555 1555 2.32 LINK ND1 HIS A 110 ZN ZN A 602 1555 1555 2.10 LINK SG CYS A 125 ZN ZN A 601 1555 1555 2.32 LINK SG CYS A 132 ZN ZN A 601 1555 1555 2.34 LINK ND1 HIS A 134 ZN ZN A 601 1555 1555 2.11 LINK SG CYS A 138 ZN ZN A 601 1555 1555 2.32 LINK SG CYS B 241 ZN ZN B 402 1555 1555 2.26 LINK SG CYS B 300 ZN ZN B 402 1555 1555 2.34 LINK SG CYS B 305 ZN ZN B 402 1555 1555 2.32 LINK ND1 HIS B 310 ZN ZN B 402 1555 1555 2.10 LINK SG CYS B 325 ZN ZN B 401 1555 1555 2.27 LINK SG CYS B 332 ZN ZN B 401 1555 1555 2.38 LINK ND1 HIS B 334 ZN ZN B 401 1555 1555 2.05 LINK SG CYS B 338 ZN ZN B 401 1555 1555 2.36 CISPEP 1 ALA A 48 PRO A 49 0 -0.17 CISPEP 2 ALA B 248 PRO B 249 0 0.15 CRYST1 117.905 117.905 84.743 90.00 90.00 120.00 P 31 2 1 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 0.008481 0.004897 0.000000 0.00000 SCALE2 0.000000 0.009793 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011800 0.00000