HEADER HYDROLASE/INHIBITOR 30-JUN-10 3NR6 TITLE CRYSTAL STRUCTURE OF XENOTROPIC MURINE LEUKEMIA VIRUS-RELATED VIRUS TITLE 2 (XMRV) PROTEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE P14; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.4.23.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOTROPIC MULV-RELATED VIRUS VP62; SOURCE 3 ORGANISM_TAXID: 373193; SOURCE 4 STRAIN: PCDNA3.1-XMRV-VP63; SOURCE 5 GENE: GAG-POL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)TONA PRARE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST-521 KEYWDS DIMER, PROTEASE, HYDROLASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.LUBKOWSKI,M.LI,A.GUSTCHINA,D.ZHOU,Z.DAUTER,A.WLODAWER REVDAT 5 03-APR-24 3NR6 1 REMARK REVDAT 4 27-DEC-23 3NR6 1 REMARK SEQADV LINK REVDAT 3 08-NOV-17 3NR6 1 REMARK REVDAT 2 09-MAR-11 3NR6 1 JRNL REVDAT 1 02-FEB-11 3NR6 0 JRNL AUTH M.LI,F.DIMAIO,D.ZHOU,A.GUSTCHINA,J.LUBKOWSKI,Z.DAUTER, JRNL AUTH 2 D.BAKER,A.WLODAWER JRNL TITL CRYSTAL STRUCTURE OF XMRV PROTEASE DIFFERS FROM THE JRNL TITL 2 STRUCTURES OF OTHER RETROPEPSINS. JRNL REF NAT.STRUCT.MOL.BIOL. V. 18 227 2011 JRNL REFN ISSN 1545-9993 JRNL PMID 21258323 JRNL DOI 10.1038/NSMB.1964 REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0104 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 15336 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 : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 815 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) : 1.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 REFLECTION IN BIN (WORKING SET) : 920 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.76 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1791 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.48000 REMARK 3 B22 (A**2) : 0.48000 REMARK 3 B33 (A**2) : -0.97000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.164 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.108 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.324 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1863 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2538 ; 1.837 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 231 ; 7.603 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 76 ;35.578 ;24.211 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 302 ;17.844 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;15.200 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 283 ; 0.145 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1408 ; 0.010 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1168 ; 2.739 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1898 ; 4.062 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 695 ; 3.676 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 639 ; 5.066 ; 3.000 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 124 REMARK 3 ORIGIN FOR THE GROUP (A): 11.1122 21.3554 14.6024 REMARK 3 T TENSOR REMARK 3 T11: 0.0545 T22: 0.0701 REMARK 3 T33: 0.0406 T12: 0.0191 REMARK 3 T13: -0.0131 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 3.2387 L22: 4.0084 REMARK 3 L33: 4.5200 L12: 0.4637 REMARK 3 L13: -1.4235 L23: -0.9411 REMARK 3 S TENSOR REMARK 3 S11: -0.0732 S12: 0.0230 S13: -0.1454 REMARK 3 S21: -0.0354 S22: 0.0143 S23: 0.1128 REMARK 3 S31: 0.1332 S32: -0.1435 S33: 0.0589 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 125 REMARK 3 ORIGIN FOR THE GROUP (A): 9.3748 22.8382 38.6955 REMARK 3 T TENSOR REMARK 3 T11: 0.1154 T22: 0.0901 REMARK 3 T33: 0.0480 T12: 0.0489 REMARK 3 T13: 0.0362 T23: 0.0470 REMARK 3 L TENSOR REMARK 3 L11: 6.7048 L22: 2.9177 REMARK 3 L33: 5.5570 L12: -1.3269 REMARK 3 L13: 2.1263 L23: 0.4850 REMARK 3 S TENSOR REMARK 3 S11: -0.1293 S12: -0.3786 S13: -0.1642 REMARK 3 S21: 0.2565 S22: 0.0793 S23: 0.1573 REMARK 3 S31: 0.0569 S32: -0.2462 S33: 0.0499 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 REMARK 4 REMARK 4 3NR6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000060177. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI-220 REMARK 200 OPTICS : MIRRORS 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 : 16141 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : 0.04400 REMARK 200 FOR THE DATA SET : 32.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.25700 REMARK 200 R SYM FOR SHELL (I) : 0.25700 REMARK 200 FOR SHELL : 3.230 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, ROSETTA REMARK 200 STARTING MODEL: ASSEMBLY OF RETROVIRAL PROTEASES REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CONCENTRATION: 10 MG/ML REMARK 280 PRECIPITANT: 0.06 M KH2PO4, 1.34 M NA2HPO4, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 63.91500 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 63.91500 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 63.91500 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 63.91500 REMARK 350 BIOMT3 4 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 MET A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 GLY A 56 REMARK 465 ALA A 57 REMARK 465 THR A 58 REMARK 465 GLY A 59 REMARK 465 LEU A 125 REMARK 465 MET B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 GLY B 6 REMARK 465 GLY B 7 REMARK 465 GLN B 8 REMARK 465 GLY B 9 REMARK 465 GLN B 10 REMARK 465 GLU B 11 REMARK 465 GLN B 55 REMARK 465 GLY B 56 REMARK 465 ALA B 57 REMARK 465 THR B 58 REMARK 465 GLY B 59 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 B 136 O HOH B 143 2.11 REMARK 500 O HOH A 159 O HOH A 162 2.16 REMARK 500 O LEU B 125 O HOH B 139 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 137 O HOH A 137 2565 2.19 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 ASP A 87 32.07 -76.89 REMARK 500 ASN B 43 70.26 29.93 REMARK 500 ASP B 87 33.40 -83.29 REMARK 500 GLU B 108 -169.98 -101.59 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 K A 126 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 5 O REMARK 620 2 GLN A 8 OE1 89.3 REMARK 620 3 PRO A 26 O 105.4 105.1 REMARK 620 4 HOH A 139 O 72.0 95.5 159.2 REMARK 620 5 HOH A 153 O 159.9 80.5 94.0 91.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 126 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 127 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HVP RELATED DB: PDB REMARK 900 HUMAN IMMUNODEFICIENCY VIRUS 1 (HIV-1) PROTEASE. RELATED RETROVIRAL, REMARK 900 ASPARTIC PROTEASE REMARK 900 RELATED ID: 4FIV RELATED DB: PDB REMARK 900 FELINE IMMUNODEFICIENCY VIRUS (FIV) PROTEASE. RELATED RETROVIRAL, REMARK 900 ASPARTIC PROTEASE REMARK 900 RELATED ID: 2FMB RELATED DB: PDB REMARK 900 EQUINE INFECTIOUS ANEMIA VIRUS (EIAV) PROTEASE. RELATED RETROVIRAL, REMARK 900 ASPARTIC PROTEASE REMARK 900 RELATED ID: 2I1A RELATED DB: PDB REMARK 900 DAMAGE-INDUCIBLE PROTEIN, DDI1. RETROVIRAL PROTEASE-LIKE DOMAIN, REMARK 900 RESIDUES 180-325 REMARK 900 RELATED ID: 2RSP RELATED DB: PDB REMARK 900 STRUCTURE OF THE ASPARTIC PROTEASE FROM ROUS SARCOMA RETROVIRUS REMARK 900 REFINED AT 2 ANGSTROMS RESOLUTION DBREF 3NR6 A 1 125 UNP A1Z651 POL_XMRV6 533 657 DBREF 3NR6 B 1 125 UNP A1Z651 POL_XMRV6 533 657 SEQADV 3NR6 MET A -6 UNP A1Z651 EXPRESSION TAG SEQADV 3NR6 HIS A -5 UNP A1Z651 EXPRESSION TAG SEQADV 3NR6 HIS A -4 UNP A1Z651 EXPRESSION TAG SEQADV 3NR6 HIS A -3 UNP A1Z651 EXPRESSION TAG SEQADV 3NR6 HIS A -2 UNP A1Z651 EXPRESSION TAG SEQADV 3NR6 HIS A -1 UNP A1Z651 EXPRESSION TAG SEQADV 3NR6 HIS A 0 UNP A1Z651 EXPRESSION TAG SEQADV 3NR6 MET B -6 UNP A1Z651 EXPRESSION TAG SEQADV 3NR6 HIS B -5 UNP A1Z651 EXPRESSION TAG SEQADV 3NR6 HIS B -4 UNP A1Z651 EXPRESSION TAG SEQADV 3NR6 HIS B -3 UNP A1Z651 EXPRESSION TAG SEQADV 3NR6 HIS B -2 UNP A1Z651 EXPRESSION TAG SEQADV 3NR6 HIS B -1 UNP A1Z651 EXPRESSION TAG SEQADV 3NR6 HIS B 0 UNP A1Z651 EXPRESSION TAG SEQRES 1 A 132 MET HIS HIS HIS HIS HIS HIS THR LEU GLY ASP GLN GLY SEQRES 2 A 132 GLY GLN GLY GLN GLU PRO PRO PRO GLU PRO ARG ILE THR SEQRES 3 A 132 LEU LYS VAL GLY GLY GLN PRO VAL THR PHE LEU VAL ASP SEQRES 4 A 132 THR GLY ALA GLN HIS SER VAL LEU THR GLN ASN PRO GLY SEQRES 5 A 132 PRO LEU SER ASP LYS SER ALA TRP VAL GLN GLY ALA THR SEQRES 6 A 132 GLY GLY LYS ARG TYR ARG TRP THR THR ASP ARG LYS VAL SEQRES 7 A 132 HIS LEU ALA THR GLY LYS VAL THR HIS SER PHE LEU HIS SEQRES 8 A 132 VAL PRO ASP CYS PRO TYR PRO LEU LEU GLY ARG ASP LEU SEQRES 9 A 132 LEU THR LYS LEU LYS ALA GLN ILE HIS PHE GLU GLY SER SEQRES 10 A 132 GLY ALA GLN VAL VAL GLY PRO MET GLY GLN PRO LEU GLN SEQRES 11 A 132 VAL LEU SEQRES 1 B 132 MET HIS HIS HIS HIS HIS HIS THR LEU GLY ASP GLN GLY SEQRES 2 B 132 GLY GLN GLY GLN GLU PRO PRO PRO GLU PRO ARG ILE THR SEQRES 3 B 132 LEU LYS VAL GLY GLY GLN PRO VAL THR PHE LEU VAL ASP SEQRES 4 B 132 THR GLY ALA GLN HIS SER VAL LEU THR GLN ASN PRO GLY SEQRES 5 B 132 PRO LEU SER ASP LYS SER ALA TRP VAL GLN GLY ALA THR SEQRES 6 B 132 GLY GLY LYS ARG TYR ARG TRP THR THR ASP ARG LYS VAL SEQRES 7 B 132 HIS LEU ALA THR GLY LYS VAL THR HIS SER PHE LEU HIS SEQRES 8 B 132 VAL PRO ASP CYS PRO TYR PRO LEU LEU GLY ARG ASP LEU SEQRES 9 B 132 LEU THR LYS LEU LYS ALA GLN ILE HIS PHE GLU GLY SER SEQRES 10 B 132 GLY ALA GLN VAL VAL GLY PRO MET GLY GLN PRO LEU GLN SEQRES 11 B 132 VAL LEU HET K A 126 1 HET PO4 A 127 5 HETNAM K POTASSIUM ION HETNAM PO4 PHOSPHATE ION FORMUL 3 K K 1+ FORMUL 4 PO4 O4 P 3- FORMUL 5 HOH *66(H2 O) HELIX 1 1 GLY A 7 GLU A 11 5 5 HELIX 2 2 GLY A 94 LYS A 102 1 9 HELIX 3 3 GLY B 94 LYS B 102 1 9 SHEET 1 A 5 GLY A 76 HIS A 80 0 SHEET 2 A 5 ARG A 69 LEU A 73 -1 N VAL A 71 O VAL A 78 SHEET 3 A 5 ARG A 17 VAL A 22 -1 N LYS A 21 O HIS A 72 SHEET 4 A 5 GLN A 25 VAL A 31 -1 O VAL A 27 N LEU A 20 SHEET 5 A 5 LEU A 92 LEU A 93 1 O LEU A 93 N LEU A 30 SHEET 1 B 2 VAL A 39 LEU A 40 0 SHEET 2 B 2 LEU A 83 HIS A 84 1 O LEU A 83 N LEU A 40 SHEET 1 C 2 LEU A 47 VAL A 54 0 SHEET 2 C 2 LYS A 61 THR A 66 -1 O LYS A 61 N VAL A 54 SHEET 1 D 4 ALA A 112 VAL A 115 0 SHEET 2 D 4 GLN A 104 PHE A 107 -1 N HIS A 106 O GLN A 113 SHEET 3 D 4 GLN B 104 GLU B 108 -1 O ILE B 105 N ILE A 105 SHEET 4 D 4 GLY B 111 VAL B 115 -1 O GLN B 113 N HIS B 106 SHEET 1 E 5 GLY B 76 HIS B 80 0 SHEET 2 E 5 ARG B 69 LEU B 73 -1 N VAL B 71 O VAL B 78 SHEET 3 E 5 ARG B 17 VAL B 22 -1 N LYS B 21 O HIS B 72 SHEET 4 E 5 GLN B 25 VAL B 31 -1 O VAL B 27 N LEU B 20 SHEET 5 E 5 LEU B 92 LEU B 93 1 O LEU B 93 N LEU B 30 SHEET 1 F 2 VAL B 39 LEU B 40 0 SHEET 2 F 2 LEU B 83 HIS B 84 1 O LEU B 83 N LEU B 40 SHEET 1 G 2 LEU B 47 TRP B 53 0 SHEET 2 G 2 ARG B 62 THR B 66 -1 O TRP B 65 N SER B 48 LINK O GLN A 5 K K A 126 1555 1555 2.80 LINK OE1 GLN A 8 K K A 126 1555 1555 2.80 LINK O PRO A 26 K K A 126 1555 1555 2.95 LINK K K A 126 O HOH A 139 1555 1555 2.93 LINK K K A 126 O HOH A 153 1555 1555 2.58 CISPEP 1 GLU A 15 PRO A 16 0 -0.30 CISPEP 2 GLU B 15 PRO B 16 0 -3.22 CISPEP 3 GLU B 15 PRO B 16 0 -2.07 SITE 1 AC1 5 GLN A 5 GLN A 8 PRO A 26 HOH A 139 SITE 2 AC1 5 HOH A 153 SITE 1 AC2 3 GLY A 6 GLY A 7 LYS A 50 CRYST1 63.915 63.915 106.509 90.00 90.00 90.00 P 4 2 2 16 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 0.015646 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015646 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009389 0.00000