HEADER HYDROLASE 27-APR-17 5NTH TITLE STRUCTURE OF LEUCYL AMINOPEPTIDASE FROM LEISHMANIA MAJOR IN COMPLEX TITLE 2 WITH ACTINONIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE AMINOPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.11.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA MAJOR; SOURCE 3 ORGANISM_TAXID: 5664; SOURCE 4 GENE: LMJF_11_0630; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS M17 LEUCYL AMINOPEPTIDASE, AMINOPEPTIDASE, LEISHMANIA MAJOR KEYWDS 2 ACTINONIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.TIMM,K.WILSON REVDAT 5 17-JAN-24 5NTH 1 LINK REVDAT 4 28-MAR-18 5NTH 1 JRNL REVDAT 3 21-FEB-18 5NTH 1 JRNL REVDAT 2 30-AUG-17 5NTH 1 JRNL REVDAT 1 02-AUG-17 5NTH 0 JRNL AUTH J.TIMM,M.VALENTE,D.GARCIA-CABALLERO,K.S.WILSON, JRNL AUTH 2 D.GONZALEZ-PACANOWSKA JRNL TITL STRUCTURAL CHARACTERIZATION OF ACIDIC M17 LEUCINE JRNL TITL 2 AMINOPEPTIDASES FROM THE TRITRYPS AND EVALUATION OF THEIR JRNL TITL 3 ROLE IN NUTRIENT STARVATION INTRYPANOSOMA BRUCEI. JRNL REF MSPHERE V. 2 2018 JRNL REFN ESSN 2379-5042 JRNL PMID 28815215 JRNL DOI 10.1128/MSPHERE.00226-17 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 86.7 REMARK 3 NUMBER OF REFLECTIONS : 20818 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1031 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1584 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.3320 REMARK 3 BIN FREE R VALUE SET COUNT : 66 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3893 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 49 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.71000 REMARK 3 B22 (A**2) : -1.71000 REMARK 3 B33 (A**2) : 5.54000 REMARK 3 B12 (A**2) : -0.85000 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): 0.465 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.285 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.248 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.400 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3999 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3726 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5427 ; 1.642 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8546 ; 1.000 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 536 ; 6.993 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 146 ;37.313 ;24.041 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 599 ;16.235 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;17.932 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 640 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4623 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 868 ; 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): 2147 ; 1.459 ; 3.302 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2146 ; 1.456 ; 3.300 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2682 ; 2.474 ; 4.948 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2683 ; 2.473 ; 4.950 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1852 ; 1.726 ; 3.438 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1853 ; 1.726 ; 3.438 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2746 ; 2.614 ; 5.084 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4414 ; 4.187 ;26.071 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4415 ; 4.187 ;26.075 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 : NULL 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 5NTH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-APR-17. REMARK 100 THE DEPOSITION ID IS D_1200004704. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97781 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21850 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 38.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.8 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.74700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 5NSK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8 M SUCCINIC ACID PH 7.0, 3 % (W/V) REMARK 280 1,5-DIAMINO-PENTANE DI-HYDROCHLORIDE, 5 MM MNSO4, 5 MM ACTINONIN, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 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 REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -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 0.00000 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 0.00000 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 0.00000 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 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 31390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 96170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -142.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 201.67826 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -174.65850 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 100.83913 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 -174.65850 REMARK 350 BIOMT2 4 0.866025 0.500000 0.000000 100.83913 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 91.49100 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 -1.000000 0.000000 201.67826 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 91.49100 REMARK 350 BIOMT1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 91.49100 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 735 LIES ON A SPECIAL POSITION. 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 2 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 MET A 5 CG SD CE REMARK 470 LYS A 6 CG CD CE NZ REMARK 470 TYR A 46 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 55 CG CD OE1 OE2 REMARK 470 GLN A 56 CG CD OE1 NE2 REMARK 470 LYS A 80 CG CD CE NZ REMARK 470 GLU A 90 CG CD OE1 OE2 REMARK 470 LYS A 95 CG CD CE NZ REMARK 470 ARG A 198 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 200 CG CD CE NZ REMARK 470 GLU A 255 CG CD OE1 OE2 REMARK 470 GLU A 258 CG CD OE1 OE2 REMARK 470 GLU A 289 CG CD OE1 OE2 REMARK 470 LYS A 292 CG CD CE NZ REMARK 470 ARG A 344 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 441 CG CD OE1 OE2 REMARK 470 ILE A 481 CG1 CG2 CD1 REMARK 470 SER A 484 OG REMARK 470 SER A 485 OG REMARK 470 SER A 486 OG REMARK 470 SER A 487 OG REMARK 470 ARG A 506 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 538 CG CD OE1 NE2 REMARK 470 HIS A 539 CG ND1 CD2 CE1 NE2 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 ARG A 111 NE - CZ - NH1 ANGL. DEV. = 3.1 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 ARG A 9 -100.16 -122.73 REMARK 500 MET A 180 -167.12 -116.09 REMARK 500 GLN A 194 19.94 56.44 REMARK 500 ASN A 318 6.78 82.72 REMARK 500 ALA A 360 150.40 178.95 REMARK 500 ASP A 372 -24.46 131.02 REMARK 500 ARG A 393 -50.48 -30.00 REMARK 500 LEU A 461 121.74 -38.79 REMARK 500 CYS A 463 65.99 -163.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 MET A 319 LYS A 320 144.91 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 A 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 299 NZ REMARK 620 2 ASP A 304 OD2 158.7 REMARK 620 3 ASP A 322 OD2 95.7 99.9 REMARK 620 4 GLU A 391 OE2 83.3 79.2 102.8 REMARK 620 5 BB2 A 604 O2 92.2 74.3 169.5 84.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 603 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 304 OD2 REMARK 620 2 ASP A 389 O 158.1 REMARK 620 3 ASP A 389 OD1 88.9 79.7 REMARK 620 4 GLU A 391 OE1 95.7 74.4 119.5 REMARK 620 5 BB2 A 604 O4 100.8 95.5 80.0 154.9 REMARK 620 6 BB2 A 604 N1 109.1 92.5 128.7 106.4 50.1 REMARK 620 7 BB2 A 604 O2 94.9 103.2 155.9 83.9 76.0 28.5 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BCT 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 MN A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BB2 A 604 DBREF 5NTH A 2 539 UNP Q4QH17 Q4QH17_LEIMA 1 538 SEQADV 5NTH TYR A 46 UNP Q4QH17 PRO 45 CONFLICT SEQRES 1 A 538 MET SER ALA MET LYS ARG PRO ARG SER ASN SER ILE VAL SEQRES 2 A 538 GLU GLU THR ALA VAL SER ALA TYR VAL GLN THR CYS THR SEQRES 3 A 538 ASN PHE LYS SER ASN VAL THR PHE THR ASP ILE SER LYS SEQRES 4 A 538 VAL SER CYS VAL ALA TYR HIS VAL LEU LEU VAL GLY ALA SEQRES 5 A 538 LEU GLU GLN LEU ARG ASP ASN SER LEU LYS SER VAL LEU SEQRES 6 A 538 PHE TYR CYS PRO ALA VAL ALA GLU ALA LEU GLN ARG VAL SEQRES 7 A 538 LYS ALA GLY SER THR VAL LYS THR LEU ALA GLU VAL PRO SEQRES 8 A 538 GLY ARG LYS GLY TYR THR GLU VAL MET VAL THR ALA LEU SEQRES 9 A 538 PRO ALA THR THR SER ARG THR ASN CYS PRO TYR ARG ALA SEQRES 10 A 538 ASP SER MET SER GLU ALA VAL ALA ALA ALA CYS GLY SER SEQRES 11 A 538 VAL GLU GLU GLY GLU VAL LEU ASP VAL TYR VAL CYS ALA SEQRES 12 A 538 PRO ALA GLY SER GLU THR ALA VAL ALA ASN ALA VAL ALA SEQRES 13 A 538 ARG ALA ALA PRO HIS SER TYR THR ALA LYS ALA GLY GLN SEQRES 14 A 538 ALA THR LYS ALA TYR MET LYS GLN ALA MET SER LEU ASN SEQRES 15 A 538 VAL VAL MET SER SER ARG ALA ALA PHE THR GLN GLU LEU SEQRES 16 A 538 VAL ARG GLY LYS SER VAL CYS VAL ALA GLU LEU GLU ALA SEQRES 17 A 538 ILE CYS THR SER VAL GLN LEU CYS GLN ARG LEU VAL ASP SEQRES 18 A 538 THR PRO PRO CYS MET LEU ASP THR VAL VAL TYR ALA GLU SEQRES 19 A 538 ILE ALA ALA ALA TYR ALA ALA GLU LEU GLY VAL ASP MET SEQRES 20 A 538 THR VAL ILE LYS GLY ASP GLU LEU ARG GLU LYS GLY TYR SEQRES 21 A 538 GLY GLY ILE TYR ALA VAL GLY LYS CYS ALA GLN TYR PRO SEQRES 22 A 538 ALA HIS LEU VAL THR LEU ARG TYR ARG ASN PRO ASN ALA SEQRES 23 A 538 ALA GLU GLY ALA LYS ASN ILE ALA MET VAL GLY LYS GLY SEQRES 24 A 538 ILE VAL TYR ASP CYS GLY GLY LEU ALA LEU LYS PRO ALA SEQRES 25 A 538 ALA HIS MET THR ASN MET LYS THR ASP MET GLY GLY SER SEQRES 26 A 538 ALA GLY VAL PHE CYS ALA PHE ILE ALA VAL VAL ARG SER SEQRES 27 A 538 MET LYS MET GLN ARG THR HIS PHE SER HIS ILE ALA ASN SEQRES 28 A 538 ILE SER VAL THR LEU CYS LEU ALA GLU ASN ALA ILE GLY SEQRES 29 A 538 PRO HIS SER TYR ARG ASN ASP ASP VAL VAL VAL MET LYS SEQRES 30 A 538 SER GLY LYS SER VAL GLU VAL MET ASN THR ASP ALA GLU SEQRES 31 A 538 GLY ARG ILE VAL LEU GLY ASP GLY VAL TYR TYR ALA THR SEQRES 32 A 538 GLY GLU GLN ASP PHE VAL PRO ASP VAL LEU ILE ASP MET SEQRES 33 A 538 ALA THR LEU THR GLY ALA GLN GLY VAL ALA THR GLY SER SEQRES 34 A 538 LYS HIS ALA GLY VAL TYR ALA SER ASP ALA GLU ALA GLU SEQRES 35 A 538 LYS ASP MET ILE SER ALA GLY LEU GLN SER GLY ASP LEU SEQRES 36 A 538 CYS TYR PRO VAL LEU TYR CYS PRO GLU TYR HIS GLU GLU SEQRES 37 A 538 VAL TYR LYS SER PRO CYS ALA ASP MET ARG ASN ILE ALA SEQRES 38 A 538 ASN SER SER SER SER ALA GLY SER SER CYS GLY GLY TYR SEQRES 39 A 538 PHE VAL GLU GLN HIS LEU SER GLU ARG PHE ARG GLY PRO SEQRES 40 A 538 PHE VAL HIS VAL ASP MET ALA TYR PRO THR SER ASN THR SEQRES 41 A 538 ALA GLY ALA THR GLY TYR GLY VAL THR LEU VAL PHE GLU SEQRES 42 A 538 PHE LEU ARG GLN HIS HET BCT A 601 4 HET MN A 602 1 HET MN A 603 1 HET BB2 A 604 27 HETNAM BCT BICARBONATE ION HETNAM MN MANGANESE (II) ION HETNAM BB2 ACTINONIN HETSYN BB2 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2- HETSYN 2 BB2 HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL- HETSYN 3 BB2 PROPYL]-AMIDE FORMUL 2 BCT C H O3 1- FORMUL 3 MN 2(MN 2+) FORMUL 5 BB2 C19 H35 N3 O5 FORMUL 6 HOH *49(H2 O) HELIX 1 AA1 SER A 12 ASN A 28 1 17 HELIX 2 AA2 ASP A 37 VAL A 41 5 5 HELIX 3 AA3 ALA A 53 ASP A 59 1 7 HELIX 4 AA4 ASN A 60 VAL A 65 5 6 HELIX 5 AA5 CYS A 69 VAL A 79 1 11 HELIX 6 AA6 ARG A 117 CYS A 129 1 13 HELIX 7 AA7 GLY A 130 VAL A 132 5 3 HELIX 8 AA8 SER A 148 ARG A 158 1 11 HELIX 9 AA9 ALA A 166 ALA A 174 5 9 HELIX 10 AB1 ARG A 189 GLN A 194 1 6 HELIX 11 AB2 CYS A 203 THR A 223 1 21 HELIX 12 AB3 ASP A 229 GLY A 245 1 17 HELIX 13 AB4 GLY A 253 LYS A 259 1 7 HELIX 14 AB5 TYR A 261 LYS A 269 1 9 HELIX 15 AB6 PRO A 312 THR A 317 1 6 HELIX 16 AB7 ASN A 318 ASP A 322 5 5 HELIX 17 AB8 MET A 323 GLN A 343 1 21 HELIX 18 AB9 GLU A 391 GLU A 406 1 16 HELIX 19 AC1 GLY A 422 GLY A 429 1 8 HELIX 20 AC2 ASP A 439 GLY A 454 1 16 HELIX 21 AC3 CYS A 463 GLU A 469 1 7 HELIX 22 AC4 ALA A 488 GLN A 499 1 12 HELIX 23 AC5 GLY A 528 GLN A 538 1 11 SHEET 1 AA1 6 VAL A 33 PHE A 35 0 SHEET 2 AA1 6 LEU A 182 MET A 186 1 O VAL A 184 N THR A 34 SHEET 3 AA1 6 LEU A 138 CYS A 143 1 N VAL A 140 O VAL A 185 SHEET 4 AA1 6 HIS A 47 GLY A 52 1 N LEU A 49 O TYR A 141 SHEET 5 AA1 6 THR A 98 ALA A 104 1 O THR A 103 N LEU A 50 SHEET 6 AA1 6 THR A 84 ALA A 89 -1 N THR A 87 O VAL A 100 SHEET 1 AA2 8 ASP A 247 LYS A 252 0 SHEET 2 AA2 8 HIS A 276 ARG A 283 -1 O THR A 279 N THR A 249 SHEET 3 AA2 8 ILE A 350 ASN A 362 -1 O LEU A 357 N VAL A 278 SHEET 4 AA2 8 LYS A 292 ASP A 304 1 N LYS A 292 O ALA A 351 SHEET 5 AA2 8 VAL A 413 ALA A 418 1 O MET A 417 N VAL A 297 SHEET 6 AA2 8 PHE A 509 ASP A 513 1 O VAL A 512 N ASP A 416 SHEET 7 AA2 8 ALA A 433 ALA A 437 -1 N GLY A 434 O ASP A 513 SHEET 8 AA2 8 CYS A 457 PRO A 459 1 O TYR A 458 N VAL A 435 SHEET 1 AA3 3 VAL A 374 VAL A 376 0 SHEET 2 AA3 3 SER A 382 GLU A 384 -1 O VAL A 383 N VAL A 375 SHEET 3 AA3 3 MET A 478 ARG A 479 1 O MET A 478 N GLU A 384 SHEET 1 AA4 2 SER A 519 ASN A 520 0 SHEET 2 AA4 2 GLY A 523 ALA A 524 -1 O GLY A 523 N ASN A 520 LINK NZ LYS A 299 MN MN A 602 1555 1555 2.00 LINK OD2 ASP A 304 MN MN A 602 1555 1555 2.69 LINK OD2 ASP A 304 MN MN A 603 1555 1555 1.95 LINK OD2 ASP A 322 MN MN A 602 1555 1555 1.89 LINK O ASP A 389 MN MN A 603 1555 1555 1.94 LINK OD1 ASP A 389 MN MN A 603 1555 1555 1.97 LINK OE2 GLU A 391 MN MN A 602 1555 1555 1.91 LINK OE1 GLU A 391 MN MN A 603 1555 1555 1.91 LINK MN MN A 602 O2 BB2 A 604 1555 1555 1.95 LINK MN MN A 603 O4 BB2 A 604 1555 1555 2.33 LINK MN MN A 603 N1 BB2 A 604 1555 1555 2.78 LINK MN MN A 603 O2 BB2 A 604 1555 1555 1.95 SITE 1 AC1 7 ASP A 389 ALA A 390 GLU A 391 GLY A 392 SITE 2 AC1 7 ARG A 393 LEU A 420 BB2 A 604 SITE 1 AC2 6 LYS A 299 ASP A 304 ASP A 322 GLU A 391 SITE 2 AC2 6 MN A 603 BB2 A 604 SITE 1 AC3 6 ASP A 304 LYS A 311 ASP A 389 GLU A 391 SITE 2 AC3 6 MN A 602 BB2 A 604 SITE 1 AC4 13 LYS A 299 ASP A 304 LYS A 311 HIS A 315 SITE 2 AC4 13 ASP A 389 GLU A 391 LEU A 420 GLY A 422 SITE 3 AC4 13 BCT A 601 MN A 602 MN A 603 HOH A 702 SITE 4 AC4 13 HOH A 722 CRYST1 116.439 116.439 91.491 90.00 90.00 120.00 P 3 2 1 6 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 0.008588 0.004958 0.000000 0.00000 SCALE2 0.000000 0.009917 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010930 0.00000