HEADER HYDROLASE 06-NOV-17 5YQ8 TITLE CRYSTAL STRUCTURE OF RETROVIRAL PROTEASE-LIKE DOMAIN OF DDI1 FROM TITLE 2 LEISHMANIA MAJOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DAMAGE INDUCIBLE PROTEIN DDI1-LIKE PROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA MAJOR; SOURCE 3 ORGANISM_TAXID: 5664; SOURCE 4 GENE: LMJF_01_0610; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS RETROPEPSIN, ASPARTIC PROTEASE, CYTOPLASMIC, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.SUGUNA,S.KUMAR REVDAT 2 22-NOV-23 5YQ8 1 REMARK REVDAT 1 19-SEP-18 5YQ8 0 JRNL AUTH S.KUMAR,K.SUGUNA JRNL TITL CRYSTAL STRUCTURE OF THE RETROVIRAL PROTEASE-LIKE DOMAIN OF JRNL TITL 2 A PROTOZOAL DNA DAMAGE-INDUCIBLE 1 PROTEIN. JRNL REF FEBS OPEN BIO V. 8 1379 2018 JRNL REFN ESSN 2211-5463 JRNL PMID 30186740 JRNL DOI 10.1002/2211-5463.12491 REMARK 2 REMARK 2 RESOLUTION. 2.25 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 21101 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1069 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1559 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.1950 REMARK 3 BIN FREE R VALUE SET COUNT : 101 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3927 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.33000 REMARK 3 B22 (A**2) : -3.10000 REMARK 3 B33 (A**2) : 1.77000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.12000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.091 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.054 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.305 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.835 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3985 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3876 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5391 ; 1.855 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8956 ; 1.095 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 506 ; 6.873 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 165 ;38.146 ;24.545 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 725 ;15.550 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;14.199 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 644 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4365 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 736 ; 0.002 ; 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): 2035 ; 1.486 ; 1.740 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2034 ; 1.479 ; 1.739 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2536 ; 2.341 ; 2.603 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2537 ; 2.340 ; 2.605 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1950 ; 1.215 ; 1.703 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1951 ; 1.215 ; 1.705 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2856 ; 1.883 ; 2.536 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 16239 ; 4.967 ;30.777 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 15840 ; 4.771 ;30.881 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 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.514 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -H,-K,L REMARK 3 TWIN FRACTION : 0.486 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 REMARK 4 REMARK 4 5YQ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1300005725. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22170 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 58.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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: 2I1A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE TRIHYDRATE, 30 % REMARK 280 POLYETHYLENE GLYCOL 1500, PH 4.5, MICROBATCH, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 40.19500 REMARK 290 SMTRY3 2 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: 2250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 ALA B 184 REMARK 465 PRO B 310 REMARK 465 ALA B 311 REMARK 465 LEU B 312 REMARK 465 ALA B 313 REMARK 465 ALA D 184 REMARK 465 PRO D 310 REMARK 465 ALA D 311 REMARK 465 LEU D 312 REMARK 465 ALA D 313 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 ARG B 216 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 230 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 232 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 267 CG CD OE1 OE2 REMARK 470 ASP B 308 CG OD1 OD2 REMARK 470 ARG C 240 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 216 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 230 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 232 CG CD NE CZ NH1 NH2 REMARK 470 GLY D 233 O REMARK 470 GLU D 267 CG CD OE1 OE2 REMARK 470 ASP D 308 CG OD1 OD2 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 459 O HOH B 478 2.05 REMARK 500 OG1 THR C 295 OD1 ASN C 300 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 OD1 ASP C 308 OH TYR D 258 2547 2.09 REMARK 500 O HOH B 460 O HOH B 490 1655 2.11 REMARK 500 REMARK 500 REMARK: NULL 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 ASP B 228 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 MET C 224 CG - SD - CE ANGL. DEV. = 11.7 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 197 -13.27 71.48 REMARK 500 ARG A 240 96.25 -64.56 REMARK 500 MET A 249 119.47 -163.89 REMARK 500 ASP A 297 -134.01 58.91 REMARK 500 PRO A 310 40.23 -88.39 REMARK 500 ALA B 235 118.51 -36.16 REMARK 500 ASN B 292 69.88 61.02 REMARK 500 ASP B 297 -119.19 56.29 REMARK 500 ASN B 307 9.48 -63.00 REMARK 500 GLN C 197 -9.40 75.83 REMARK 500 ALA C 235 44.92 -101.39 REMARK 500 MET C 249 120.89 -176.29 REMARK 500 ALA C 255 40.46 73.78 REMARK 500 ASP C 297 -120.64 56.97 REMARK 500 LEU C 312 79.80 -107.46 REMARK 500 ALA D 235 97.92 -64.25 REMARK 500 VAL D 238 -10.26 83.33 REMARK 500 ASP D 297 -123.15 52.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 533 DISTANCE = 7.39 ANGSTROMS REMARK 525 HOH A 534 DISTANCE = 7.46 ANGSTROMS REMARK 525 HOH A 535 DISTANCE = 7.72 ANGSTROMS REMARK 525 HOH A 536 DISTANCE = 8.30 ANGSTROMS REMARK 525 HOH A 537 DISTANCE = 8.35 ANGSTROMS REMARK 525 HOH B 509 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH B 510 DISTANCE = 6.76 ANGSTROMS REMARK 525 HOH B 511 DISTANCE = 7.08 ANGSTROMS REMARK 525 HOH C 526 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH C 527 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH D 505 DISTANCE = 5.81 ANGSTROMS DBREF 5YQ8 A 184 313 UNP E9AC52 E9AC52_LEIMA 37 166 DBREF 5YQ8 B 184 313 UNP E9AC52 E9AC52_LEIMA 37 166 DBREF 5YQ8 C 184 313 UNP E9AC52 E9AC52_LEIMA 37 166 DBREF 5YQ8 D 184 313 UNP E9AC52 E9AC52_LEIMA 37 166 SEQRES 1 A 130 ALA LYS VAL THR MET LEU TYR VAL PRO CYS THR ILE ASN SEQRES 2 A 130 GLN VAL LEU VAL LYS ALA PHE VAL ASP SER GLY ALA GLN SEQRES 3 A 130 ASN SER ILE MET ASN LYS ARG THR ALA GLU ARG CYS GLY SEQRES 4 A 130 LEU MET ARG LEU VAL ASP VAL ARG MET ARG GLY VAL ALA SEQRES 5 A 130 VAL GLY VAL GLY ARG GLN GLU ILE CYS GLY ARG ILE HIS SEQRES 6 A 130 MET THR PRO VAL ASN LEU ALA GLY MET TYR ILE PRO PHE SEQRES 7 A 130 ALA PHE TYR VAL ILE GLU ASP GLN ALA MET ASP LEU ILE SEQRES 8 A 130 ILE GLY LEU ASP GLN LEU LYS ARG HIS GLN MET MET ILE SEQRES 9 A 130 ASP LEU LYS HIS ASN CYS LEU THR ILE ASP ASN ILE ASN SEQRES 10 A 130 VAL PRO PHE LEU PRO GLU ASN ASP LEU PRO ALA LEU ALA SEQRES 1 B 130 ALA LYS VAL THR MET LEU TYR VAL PRO CYS THR ILE ASN SEQRES 2 B 130 GLN VAL LEU VAL LYS ALA PHE VAL ASP SER GLY ALA GLN SEQRES 3 B 130 ASN SER ILE MET ASN LYS ARG THR ALA GLU ARG CYS GLY SEQRES 4 B 130 LEU MET ARG LEU VAL ASP VAL ARG MET ARG GLY VAL ALA SEQRES 5 B 130 VAL GLY VAL GLY ARG GLN GLU ILE CYS GLY ARG ILE HIS SEQRES 6 B 130 MET THR PRO VAL ASN LEU ALA GLY MET TYR ILE PRO PHE SEQRES 7 B 130 ALA PHE TYR VAL ILE GLU ASP GLN ALA MET ASP LEU ILE SEQRES 8 B 130 ILE GLY LEU ASP GLN LEU LYS ARG HIS GLN MET MET ILE SEQRES 9 B 130 ASP LEU LYS HIS ASN CYS LEU THR ILE ASP ASN ILE ASN SEQRES 10 B 130 VAL PRO PHE LEU PRO GLU ASN ASP LEU PRO ALA LEU ALA SEQRES 1 C 130 ALA LYS VAL THR MET LEU TYR VAL PRO CYS THR ILE ASN SEQRES 2 C 130 GLN VAL LEU VAL LYS ALA PHE VAL ASP SER GLY ALA GLN SEQRES 3 C 130 ASN SER ILE MET ASN LYS ARG THR ALA GLU ARG CYS GLY SEQRES 4 C 130 LEU MET ARG LEU VAL ASP VAL ARG MET ARG GLY VAL ALA SEQRES 5 C 130 VAL GLY VAL GLY ARG GLN GLU ILE CYS GLY ARG ILE HIS SEQRES 6 C 130 MET THR PRO VAL ASN LEU ALA GLY MET TYR ILE PRO PHE SEQRES 7 C 130 ALA PHE TYR VAL ILE GLU ASP GLN ALA MET ASP LEU ILE SEQRES 8 C 130 ILE GLY LEU ASP GLN LEU LYS ARG HIS GLN MET MET ILE SEQRES 9 C 130 ASP LEU LYS HIS ASN CYS LEU THR ILE ASP ASN ILE ASN SEQRES 10 C 130 VAL PRO PHE LEU PRO GLU ASN ASP LEU PRO ALA LEU ALA SEQRES 1 D 130 ALA LYS VAL THR MET LEU TYR VAL PRO CYS THR ILE ASN SEQRES 2 D 130 GLN VAL LEU VAL LYS ALA PHE VAL ASP SER GLY ALA GLN SEQRES 3 D 130 ASN SER ILE MET ASN LYS ARG THR ALA GLU ARG CYS GLY SEQRES 4 D 130 LEU MET ARG LEU VAL ASP VAL ARG MET ARG GLY VAL ALA SEQRES 5 D 130 VAL GLY VAL GLY ARG GLN GLU ILE CYS GLY ARG ILE HIS SEQRES 6 D 130 MET THR PRO VAL ASN LEU ALA GLY MET TYR ILE PRO PHE SEQRES 7 D 130 ALA PHE TYR VAL ILE GLU ASP GLN ALA MET ASP LEU ILE SEQRES 8 D 130 ILE GLY LEU ASP GLN LEU LYS ARG HIS GLN MET MET ILE SEQRES 9 D 130 ASP LEU LYS HIS ASN CYS LEU THR ILE ASP ASN ILE ASN SEQRES 10 D 130 VAL PRO PHE LEU PRO GLU ASN ASP LEU PRO ALA LEU ALA FORMUL 5 HOH *480(H2 O) HELIX 1 AA1 LYS A 215 CYS A 221 1 7 HELIX 2 AA2 LEU A 223 VAL A 227 5 5 HELIX 3 AA3 GLY A 276 HIS A 283 1 8 HELIX 4 AA4 PRO A 305 LEU A 309 5 5 HELIX 5 AA5 LYS B 215 GLY B 222 1 8 HELIX 6 AA6 GLY B 276 HIS B 283 1 8 HELIX 7 AA7 LYS C 215 CYS C 221 1 7 HELIX 8 AA8 VAL C 229 ARG C 232 5 4 HELIX 9 AA9 GLY C 276 HIS C 283 1 8 HELIX 10 AB1 PRO C 305 LEU C 309 5 5 HELIX 11 AB2 LYS D 215 CYS D 221 1 7 HELIX 12 AB3 ASP D 228 ARG D 232 5 5 HELIX 13 AB4 GLY D 276 HIS D 283 1 8 SHEET 1 AA1 7 TYR A 190 ILE A 195 0 SHEET 2 AA1 7 VAL A 198 VAL A 204 -1 O VAL A 200 N CYS A 193 SHEET 3 AA1 7 LEU A 273 ILE A 275 1 O ILE A 275 N PHE A 203 SHEET 4 AA1 7 ILE A 212 ASN A 214 -1 N ILE A 212 O ILE A 274 SHEET 5 AA1 7 MET A 257 ILE A 266 1 O TYR A 264 N MET A 213 SHEET 6 AA1 7 GLY A 245 LEU A 254 -1 N ILE A 247 O PHE A 263 SHEET 7 AA1 7 TYR A 190 ILE A 195 -1 N THR A 194 O ASN A 253 SHEET 1 AA2 6 ILE A 299 PRO A 302 0 SHEET 2 AA2 6 CYS A 293 ILE A 296 -1 N LEU A 294 O VAL A 301 SHEET 3 AA2 6 MET A 286 ASP A 288 -1 N MET A 286 O THR A 295 SHEET 4 AA2 6 MET B 286 ASP B 288 -1 O ILE B 287 N ILE A 287 SHEET 5 AA2 6 CYS B 293 ILE B 296 -1 O CYS B 293 N ASP B 288 SHEET 6 AA2 6 ILE B 299 PRO B 302 -1 O ILE B 299 N ILE B 296 SHEET 1 AA3 7 TYR B 190 ILE B 195 0 SHEET 2 AA3 7 LEU B 199 VAL B 204 -1 O VAL B 200 N CYS B 193 SHEET 3 AA3 7 LEU B 273 ILE B 275 1 O LEU B 273 N PHE B 203 SHEET 4 AA3 7 ILE B 212 ASN B 214 -1 N ILE B 212 O ILE B 274 SHEET 5 AA3 7 MET B 257 ILE B 266 1 O TYR B 264 N MET B 213 SHEET 6 AA3 7 ILE B 243 LEU B 254 -1 N LEU B 254 O MET B 257 SHEET 7 AA3 7 TYR B 190 ILE B 195 -1 N THR B 194 O ASN B 253 SHEET 1 AA4 8 VAL C 227 ASP C 228 0 SHEET 2 AA4 8 GLY C 245 LEU C 254 -1 O ARG C 246 N ASP C 228 SHEET 3 AA4 8 MET C 257 ILE C 266 -1 O VAL C 265 N GLY C 245 SHEET 4 AA4 8 ILE C 212 ASN C 214 1 N MET C 213 O TYR C 264 SHEET 5 AA4 8 LEU C 273 ILE C 275 -1 O ILE C 274 N ILE C 212 SHEET 6 AA4 8 VAL C 198 VAL C 204 1 N PHE C 203 O ILE C 275 SHEET 7 AA4 8 TYR C 190 ILE C 195 -1 N VAL C 191 O ALA C 202 SHEET 8 AA4 8 GLY C 245 LEU C 254 -1 O ASN C 253 N THR C 194 SHEET 1 AA5 6 ILE C 299 PRO C 302 0 SHEET 2 AA5 6 CYS C 293 ILE C 296 -1 N LEU C 294 O VAL C 301 SHEET 3 AA5 6 MET C 286 ASP C 288 -1 N MET C 286 O THR C 295 SHEET 4 AA5 6 MET D 285 ASP D 288 -1 O ILE D 287 N ILE C 287 SHEET 5 AA5 6 CYS D 293 ILE D 296 -1 O THR D 295 N MET D 286 SHEET 6 AA5 6 ILE D 299 PRO D 302 -1 O VAL D 301 N LEU D 294 SHEET 1 AA6 7 TYR D 190 ILE D 195 0 SHEET 2 AA6 7 VAL D 198 VAL D 204 -1 O ALA D 202 N VAL D 191 SHEET 3 AA6 7 LEU D 273 ILE D 275 1 O ILE D 275 N PHE D 203 SHEET 4 AA6 7 ILE D 212 ASN D 214 -1 N ILE D 212 O ILE D 274 SHEET 5 AA6 7 MET D 257 ILE D 266 1 O TYR D 264 N MET D 213 SHEET 6 AA6 7 ILE D 243 LEU D 254 -1 N GLY D 245 O VAL D 265 SHEET 7 AA6 7 TYR D 190 ILE D 195 -1 N THR D 194 O ASN D 253 CRYST1 35.530 80.390 85.450 90.00 90.00 90.00 P 1 21 1 8 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 0.028145 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012439 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011703 0.00000