HEADER HYDROLASE/HYDROLASE INHIBITOR 12-DEC-17 6BV5 TITLE STRUCTURE OF PROTEINACEOUS RNASE P 1 (PRORP1) FROM A. THALIANA AFTER TITLE 2 45-MINUTE SOAK WITH JUGLONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEINACEOUS RNASE P 1, CHLOROPLASTIC/MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 77-572; COMPND 5 SYNONYM: PROTEINACEOUS RNASE P 1, PENTATRICOPEPTIDE REPEAT-CONTAINING COMPND 6 PROTEIN AT2G32230; COMPND 7 EC: 3.1.26.5; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: PRORP1, AT2G32230, F22D22.2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETM-11 KEYWDS METALLONUCLEASE, PRORP, RIBONUCLEASE, PIN, TRNA PROCESSING, RNASE P, KEYWDS 2 NYN DOMAIN, PPR DOMAIN, CHLOROPLASTS, MITOCHONDRIA, HYDROLASE- KEYWDS 3 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.KARASIK,N.WU,C.A.FIERKE,M.KOUTMOS REVDAT 4 09-OCT-24 6BV5 1 REMARK REVDAT 3 04-OCT-23 6BV5 1 LINK REVDAT 2 01-JAN-20 6BV5 1 REMARK REVDAT 1 12-JUN-19 6BV5 0 JRNL AUTH N.WU,A.KARASIK,L.MUEHLBAUER,M.KOUTMOS,C.A.FIERKE JRNL TITL INHIBITION OF PROTEIN-ONLY RNASE P WITH GAMBOGIC ACID AND JRNL TITL 2 JUGLONE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 87.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 57980 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3033 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) : 1.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4149 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 202 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3767 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 239 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.41000 REMARK 3 B22 (A**2) : 1.09000 REMARK 3 B33 (A**2) : -0.68000 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): 0.111 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3873 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3750 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5228 ; 1.284 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8551 ; 0.893 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 470 ; 5.582 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 182 ;33.459 ;24.121 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 697 ;12.370 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;18.231 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 561 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4347 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 883 ; 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): 1887 ; 2.469 ; 4.618 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1886 ; 2.465 ; 4.616 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2350 ; 3.573 ; 6.911 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2351 ; 3.572 ; 6.913 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1986 ; 2.922 ; 4.963 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1987 ; 2.921 ; 4.965 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2878 ; 4.731 ; 7.276 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4464 ; 6.369 ;53.286 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4396 ; 6.315 ;53.200 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 : BABINET MODEL WITH 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 6BV5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1000230269. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033200 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : K-B PAIR OF BIOMORPH MIRRORS FOR REMARK 200 VERTICAL AND HORIZONTAL FOCUSING REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61385 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 87.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.47800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: PDB ENTRY 4G23 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG3350, 0.1 M SODIUM CITRATE REMARK 280 TRIBASIC, PH 5.5, VAPOR DIFFUSION, SITTING 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 20.80800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.37150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.41900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.37150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.80800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.41900 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: 530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 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 72 REMARK 465 ALA A 73 REMARK 465 GLY A 74 REMARK 465 HIS A 75 REMARK 465 MET A 76 REMARK 465 ALA A 77 REMARK 465 SER A 78 REMARK 465 PRO A 79 REMARK 465 SER A 80 REMARK 465 GLU A 81 REMARK 465 ASN A 82 REMARK 465 LEU A 83 REMARK 465 SER A 84 REMARK 465 ARG A 85 REMARK 465 LYS A 86 REMARK 465 ALA A 87 REMARK 465 LYS A 88 REMARK 465 LYS A 89 REMARK 465 LYS A 90 REMARK 465 ALA A 91 REMARK 465 ILE A 92 REMARK 465 GLN A 93 REMARK 465 GLN A 94 REMARK 465 ASN A 443 REMARK 465 GLY A 444 REMARK 465 GLY A 445 REMARK 465 PRO A 446 REMARK 465 THR A 571 REMARK 465 PRO A 572 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 916 O HOH A 920 2.10 REMARK 500 O HOH A 931 O HOH A 937 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 ARG A 277 -57.07 72.40 REMARK 500 ARG A 277 -54.26 70.13 REMARK 500 HIS A 321 -33.64 -133.44 REMARK 500 HIS A 498 -124.99 52.90 REMARK 500 SER A 506 -74.01 -123.00 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 ZN A 603 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 344 SG REMARK 620 2 CYS A 347 SG 113.6 REMARK 620 3 HIS A 548 NE2 105.3 102.8 REMARK 620 4 CYS A 565 SG 109.7 114.7 110.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 475 OD1 REMARK 620 2 HOH A 703 O 91.1 REMARK 620 3 HOH A 708 O 85.8 83.3 REMARK 620 4 HOH A 715 O 86.6 175.4 92.6 REMARK 620 5 HOH A 756 O 102.3 89.4 169.2 95.0 REMARK 620 6 HOH A 930 O 172.2 91.3 87.1 90.5 85.1 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 JUG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 605 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6BV6 RELATED DB: PDB REMARK 900 RELATED ID: 6BV8 RELATED DB: PDB REMARK 900 RELATED ID: 6BV9 RELATED DB: PDB DBREF 6BV5 A 77 572 UNP Q66GI4 PRRP1_ARATH 77 572 SEQADV 6BV5 GLY A 72 UNP Q66GI4 EXPRESSION TAG SEQADV 6BV5 ALA A 73 UNP Q66GI4 EXPRESSION TAG SEQADV 6BV5 GLY A 74 UNP Q66GI4 EXPRESSION TAG SEQADV 6BV5 HIS A 75 UNP Q66GI4 EXPRESSION TAG SEQADV 6BV5 MET A 76 UNP Q66GI4 EXPRESSION TAG SEQRES 1 A 501 GLY ALA GLY HIS MET ALA SER PRO SER GLU ASN LEU SER SEQRES 2 A 501 ARG LYS ALA LYS LYS LYS ALA ILE GLN GLN SER PRO GLU SEQRES 3 A 501 ALA LEU LEU LYS GLN LYS LEU ASP MET CYS SER LYS LYS SEQRES 4 A 501 GLY ASP VAL LEU GLU ALA LEU ARG LEU TYR ASP GLU ALA SEQRES 5 A 501 ARG ARG ASN GLY VAL GLN LEU SER GLN TYR HIS TYR ASN SEQRES 6 A 501 VAL LEU LEU TYR VAL CYS SER LEU ALA GLU ALA ALA THR SEQRES 7 A 501 GLU SER SER PRO ASN PRO GLY LEU SER ARG GLY PHE ASP SEQRES 8 A 501 ILE PHE LYS GLN MET ILE VAL ASP LYS VAL VAL PRO ASN SEQRES 9 A 501 GLU ALA THR PHE THR ASN GLY ALA ARG LEU ALA VAL ALA SEQRES 10 A 501 LYS ASP ASP PRO GLU MET ALA PHE ASP MET VAL LYS GLN SEQRES 11 A 501 MET LYS ALA PHE GLY ILE GLN PRO ARG LEU ARG SER TYR SEQRES 12 A 501 GLY PRO ALA LEU PHE GLY PHE CYS ARG LYS GLY ASP ALA SEQRES 13 A 501 ASP LYS ALA TYR GLU VAL ASP ALA HIS MET VAL GLU SER SEQRES 14 A 501 GLU VAL VAL PRO GLU GLU PRO GLU LEU ALA ALA LEU LEU SEQRES 15 A 501 LYS VAL SER MET ASP THR LYS ASN ALA ASP LYS VAL TYR SEQRES 16 A 501 LYS THR LEU GLN ARG LEU ARG ASP LEU VAL ARG GLN VAL SEQRES 17 A 501 SER LYS SER THR PHE ASP MET ILE GLU GLU TRP PHE LYS SEQRES 18 A 501 SER GLU VAL ALA THR LYS THR GLY VAL LYS LYS TRP ASP SEQRES 19 A 501 VAL LYS LYS ILE ARG ASP ALA VAL VAL SER GLY GLY GLY SEQRES 20 A 501 GLY TRP HIS GLY GLN GLY TRP LEU GLY THR GLY LYS TRP SEQRES 21 A 501 ASN VAL LYS ARG THR GLU MET ASP GLU ASN GLY VAL CYS SEQRES 22 A 501 LYS CYS CYS LYS GLU LYS LEU VAL CYS ILE ASP ILE ASN SEQRES 23 A 501 PRO VAL GLU THR GLU THR PHE ALA ALA SER LEU THR ARG SEQRES 24 A 501 LEU ALA CYS GLU ARG GLU VAL LYS ALA ASN PHE ASN GLN SEQRES 25 A 501 PHE GLN GLU TRP LEU GLU ARG HIS GLY PRO PHE ASP ALA SEQRES 26 A 501 VAL ILE ASP GLY ALA ASN MET GLY LEU VAL ASN GLN ARG SEQRES 27 A 501 SER PHE SER PHE PHE GLN LEU ASN ASN THR VAL GLN ARG SEQRES 28 A 501 CYS GLN GLN ILE SER PRO SER LYS ARG LEU PRO LEU VAL SEQRES 29 A 501 ILE LEU HIS LYS SER ARG VAL ASN GLY GLY PRO ALA THR SEQRES 30 A 501 TYR PRO LYS ASN ARG ALA LEU LEU GLU LYS TRP LYS ASN SEQRES 31 A 501 ALA GLY ALA LEU TYR ALA THR PRO PRO GLY SER ASN ASP SEQRES 32 A 501 ASP TRP TYR TRP LEU TYR ALA ALA VAL SER CYS LYS CYS SEQRES 33 A 501 LEU LEU VAL THR ASN ASP GLU MET ARG ASP HIS LEU PHE SEQRES 34 A 501 GLN LEU LEU GLY ASN SER PHE PHE PRO ARG TRP LYS GLU SEQRES 35 A 501 LYS HIS GLN VAL ARG ILE SER VAL THR ARG GLU ASP GLY SEQRES 36 A 501 LEU LYS LEU ASN MET PRO PRO PRO TYR SER ILE VAL ILE SEQRES 37 A 501 GLN GLU SER GLU ASP GLY THR TRP HIS VAL PRO MET SER SEQRES 38 A 501 VAL GLU ASP ASP LEU GLN THR SER ARG GLN TRP LEU CYS SEQRES 39 A 501 ALA LYS ARG SER LYS THR PRO HET JUG A 601 13 HET MN A 602 1 HET ZN A 603 1 HET CL A 604 1 HET CL A 605 1 HETNAM JUG 5-HYDROXYNAPHTHALENE-1,4-DIONE HETNAM MN MANGANESE (II) ION HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETSYN JUG JUGLONE FORMUL 2 JUG C10 H6 O3 FORMUL 3 MN MN 2+ FORMUL 4 ZN ZN 2+ FORMUL 5 CL 2(CL 1-) FORMUL 7 HOH *239(H2 O) HELIX 1 AA1 SER A 95 GLY A 111 1 17 HELIX 2 AA2 ASP A 112 GLY A 127 1 16 HELIX 3 AA3 SER A 131 LEU A 144 1 14 HELIX 4 AA4 ASN A 154 ASP A 170 1 17 HELIX 5 AA5 ASN A 175 ASP A 190 1 16 HELIX 6 AA6 ASP A 191 PHE A 205 1 15 HELIX 7 AA7 ARG A 210 LYS A 224 1 15 HELIX 8 AA8 ASP A 226 SER A 240 1 15 HELIX 9 AA9 GLU A 245 THR A 259 1 15 HELIX 10 AB1 ASN A 261 VAL A 276 1 16 HELIX 11 AB2 SER A 280 SER A 293 1 14 HELIX 12 AB3 SER A 293 THR A 299 1 7 HELIX 13 AB4 ASP A 305 GLY A 316 1 12 HELIX 14 AB5 ASN A 357 GLU A 376 1 20 HELIX 15 AB6 VAL A 377 ARG A 390 1 14 HELIX 16 AB7 GLY A 400 VAL A 406 1 7 HELIX 17 AB8 SER A 412 SER A 427 1 16 HELIX 18 AB9 TYR A 449 ALA A 462 1 14 HELIX 19 AC1 ASP A 474 LYS A 486 1 13 HELIX 20 AC2 ASP A 497 GLY A 504 5 8 HELIX 21 AC3 SER A 506 HIS A 515 1 10 SHEET 1 AA1 4 TRP A 331 THR A 336 0 SHEET 2 AA1 4 TRP A 563 ARG A 568 -1 O LYS A 567 N ASN A 332 SHEET 3 AA1 4 TRP A 547 PRO A 550 -1 N TRP A 547 O ALA A 566 SHEET 4 AA1 4 GLN A 540 GLU A 541 -1 N GLN A 540 O HIS A 548 SHEET 1 AA2 6 LEU A 465 THR A 468 0 SHEET 2 AA2 6 LEU A 434 HIS A 438 1 N LEU A 437 O THR A 468 SHEET 3 AA2 6 ALA A 396 ASP A 399 1 N ILE A 398 O LEU A 434 SHEET 4 AA2 6 LEU A 488 VAL A 490 1 O VAL A 490 N VAL A 397 SHEET 5 AA2 6 GLN A 516 THR A 522 1 O VAL A 517 N LEU A 489 SHEET 6 AA2 6 GLY A 526 ASN A 530 -1 O ASN A 530 N ARG A 518 LINK SG CYS A 353 CAG JUG A 601 1555 1555 1.72 LINK SG CYS A 344 ZN ZN A 603 1555 1555 2.35 LINK SG CYS A 347 ZN ZN A 603 1555 1555 2.18 LINK OD1 ASP A 475 MN MN A 602 1555 1555 2.20 LINK NE2 HIS A 548 ZN ZN A 603 1555 1555 2.08 LINK SG CYS A 565 ZN ZN A 603 1555 1555 2.31 LINK MN MN A 602 O HOH A 703 1555 1555 2.22 LINK MN MN A 602 O HOH A 708 1555 1555 1.98 LINK MN MN A 602 O HOH A 715 1555 1555 2.28 LINK MN MN A 602 O HOH A 756 1555 1555 2.15 LINK MN MN A 602 O HOH A 930 1555 1555 2.29 CISPEP 1 GLY A 392 PRO A 393 0 6.62 SITE 1 AC1 4 CYS A 353 LYS A 514 PRO A 533 PRO A 534 SITE 1 AC2 6 ASP A 475 HOH A 703 HOH A 708 HOH A 715 SITE 2 AC2 6 HOH A 756 HOH A 930 SITE 1 AC3 4 CYS A 344 CYS A 347 HIS A 548 CYS A 565 SITE 1 AC4 5 PRO A 393 PHE A 394 LYS A 451 CYS A 485 SITE 2 AC4 5 ARG A 523 SITE 1 AC5 3 ARG A 431 PRO A 450 LYS A 451 CRYST1 41.616 110.838 140.743 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 0.024029 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009022 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007105 0.00000