HEADER HYDROLASE 27-FEB-18 5ZEH TITLE CRYSTAL STRUCTURE OF ENTAMOEBA HISTOLYTICA ARGINASE IN COMPLEX WITH L- TITLE 2 ORNITHINE AT 2.35 A COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARGINASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.5.3.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTAMOEBA HISTOLYTICA; SOURCE 3 ORGANISM_TAXID: 5759; SOURCE 4 GENE: EHI_152330; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA DE3 KEYWDS METALLOENZYME, INHIBITION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.MALIK,V.DALAL,S.ANKRI,S.TOMAR REVDAT 3 27-MAR-24 5ZEH 1 LINK REVDAT 2 06-NOV-19 5ZEH 1 JRNL REVDAT 1 26-JUN-19 5ZEH 0 JRNL AUTH A.MALIK,V.DALAL,S.ANKRI,S.TOMAR JRNL TITL STRUCTURAL INSIGHTS INTO ENTAMOEBA HISTOLYTICA ARGINASE AND JRNL TITL 2 STRUCTURE-BASED IDENTIFICATION OF NOVEL NON-AMINO ACID BASED JRNL TITL 3 INHIBITORS AS POTENTIAL ANTIAMOEBIC MOLECULES. JRNL REF FEBS J. V. 286 4135 2019 JRNL REFN ISSN 1742-464X JRNL PMID 31199070 JRNL DOI 10.1111/FEBS.14960 REMARK 2 REMARK 2 RESOLUTION. 2.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 2.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 78.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 21808 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1152 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) : 2.36 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.42 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1514 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.4050 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.4560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4567 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.74000 REMARK 3 B22 (A**2) : -1.91000 REMARK 3 B33 (A**2) : 0.16000 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): 0.659 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.296 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.369 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 37.066 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4695 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4489 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6340 ; 1.357 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10491 ; 0.942 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 588 ; 6.730 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 198 ;39.476 ;25.960 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 864 ;14.718 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;11.820 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 718 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5142 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 822 ; 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): 2364 ; 0.364 ; 2.650 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2364 ; 0.361 ; 2.650 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2948 ; 0.655 ; 3.964 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2949 ; 0.656 ; 3.966 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2331 ; 0.261 ; 2.685 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2331 ; 0.260 ; 2.685 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3393 ; 0.478 ; 4.010 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5226 ; 4.336 ;31.859 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5227 ; 4.336 ;31.876 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 293 B 1 293 19608 0.07 0.05 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 294 REMARK 3 ORIGIN FOR THE GROUP (A): -0.7130 5.0700 -8.9770 REMARK 3 T TENSOR REMARK 3 T11: 0.1132 T22: 0.2738 REMARK 3 T33: 1.0137 T12: 0.0574 REMARK 3 T13: 0.0361 T23: 0.0024 REMARK 3 L TENSOR REMARK 3 L11: 1.9862 L22: 3.1776 REMARK 3 L33: 1.1166 L12: 0.0341 REMARK 3 L13: 0.0186 L23: 0.0824 REMARK 3 S TENSOR REMARK 3 S11: -0.0289 S12: -0.1278 S13: 0.0589 REMARK 3 S21: 0.5137 S22: 0.0539 S23: 0.0388 REMARK 3 S31: -0.0275 S32: -0.0230 S33: -0.0250 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 294 REMARK 3 ORIGIN FOR THE GROUP (A): 24.5070 -22.8090 -24.4990 REMARK 3 T TENSOR REMARK 3 T11: 0.0072 T22: 0.2781 REMARK 3 T33: 0.9839 T12: -0.0015 REMARK 3 T13: -0.0032 T23: -0.0263 REMARK 3 L TENSOR REMARK 3 L11: 2.3713 L22: 4.1579 REMARK 3 L33: 1.1163 L12: -0.0158 REMARK 3 L13: -0.2781 L23: 0.0812 REMARK 3 S TENSOR REMARK 3 S11: -0.0872 S12: 0.0727 S13: -0.0853 REMARK 3 S21: 0.1090 S22: 0.0860 S23: -0.3021 REMARK 3 S31: -0.0239 S32: 0.0337 S33: 0.0012 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5ZEH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300006918. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976251 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 X 1M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22967 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 78.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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 (%): 43.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BISTRIS PROPANE (PH-9.3), 0.2M REMARK 280 POTASSIUM THIOCYANATE, 21% PEG6000, PH 9.3, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 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 43.80250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.62750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.74700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.62750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.80250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.74700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 43.80250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.74700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 66.62750 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.74700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.80250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 66.62750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 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 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 SER A 0 REMARK 465 LYS A 295 REMARK 465 CYS A 296 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 GLU B -6 REMARK 465 ASN B -5 REMARK 465 LEU B -4 REMARK 465 TYR B -3 REMARK 465 PHE B -2 REMARK 465 LEU B 59 REMARK 465 GLY B 60 REMARK 465 VAL B 61 REMARK 465 LYS B 295 REMARK 465 CYS B 296 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 GLN B -1 CB CG CD OE1 NE2 REMARK 470 SER B 0 CB OG 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 175 -54.28 -145.07 REMARK 500 GLU A 277 -66.76 -104.90 REMARK 500 SER B 0 -155.88 73.47 REMARK 500 ARG B 175 -54.57 -145.42 REMARK 500 GLU B 277 -67.27 -104.75 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 B 436 DISTANCE = 6.41 ANGSTROMS 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 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 98 ND1 REMARK 620 2 ASP A 124 OD2 83.0 REMARK 620 3 ASP A 128 OD2 92.8 90.5 REMARK 620 4 ASP A 225 OD2 88.8 71.6 161.7 REMARK 620 5 HOH A 401 O 140.1 106.7 124.9 59.9 REMARK 620 6 HOH A 406 O 110.4 165.9 93.2 103.3 60.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 303 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD1 REMARK 620 2 HIS A 126 ND1 96.2 REMARK 620 3 ASP A 225 OD2 81.2 145.0 REMARK 620 4 ASP A 227 OD1 104.1 90.6 124.1 REMARK 620 5 ASP A 227 OD2 144.3 108.0 92.5 51.3 REMARK 620 6 HOH A 401 O 111.1 86.6 62.6 144.8 96.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 98 ND1 REMARK 620 2 ASP B 124 OD2 84.1 REMARK 620 3 ASP B 128 OD2 93.3 91.4 REMARK 620 4 ASP B 225 OD2 86.2 81.3 172.6 REMARK 620 5 HOH B 402 O 140.2 113.8 120.0 63.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 303 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 124 OD1 REMARK 620 2 HIS B 126 ND1 89.9 REMARK 620 3 ASP B 225 OD2 88.1 164.7 REMARK 620 4 ASP B 227 OD1 88.5 98.2 97.0 REMARK 620 5 ASP B 227 OD2 138.7 99.4 92.1 50.4 REMARK 620 6 HOH B 402 O 109.3 101.1 65.4 153.6 108.2 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 ORN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ORN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 303 DBREF 5ZEH A 1 296 UNP C4LSS0 C4LSS0_ENTHI 1 296 DBREF 5ZEH B 1 296 UNP C4LSS0 C4LSS0_ENTHI 1 296 SEQADV 5ZEH HIS A -15 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH HIS A -14 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH HIS A -13 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH HIS A -12 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH HIS A -11 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH HIS A -10 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH SER A -9 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH SER A -8 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH GLY A -7 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH GLU A -6 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH ASN A -5 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH LEU A -4 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH TYR A -3 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH PHE A -2 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH GLN A -1 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH SER A 0 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH HIS B -15 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH HIS B -14 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH HIS B -13 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH HIS B -12 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH HIS B -11 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH HIS B -10 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH SER B -9 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH SER B -8 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH GLY B -7 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH GLU B -6 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH ASN B -5 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH LEU B -4 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH TYR B -3 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH PHE B -2 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH GLN B -1 UNP C4LSS0 EXPRESSION TAG SEQADV 5ZEH SER B 0 UNP C4LSS0 EXPRESSION TAG SEQRES 1 A 312 HIS HIS HIS HIS HIS HIS SER SER GLY GLU ASN LEU TYR SEQRES 2 A 312 PHE GLN SER MET GLN PHE GLU LYS VAL THR TYR ILE ALA SEQRES 3 A 312 VAL PRO GLN LYS TYR GLY GLN LYS LYS VAL GLY VAL GLU SEQRES 4 A 312 GLU GLY PRO LYS PHE LEU GLU LYS LEU GLY PHE MET ASN SEQRES 5 A 312 VAL LEU GLU GLN VAL ALA LYS SER VAL ASN LYS LYS THR SEQRES 6 A 312 ILE THR GLU PRO LYS THR PRO GLN GLU LEU GLY VAL THR SEQRES 7 A 312 ASN ALA ARG ASN LEU ASN GLU VAL GLU SER VAL ASN ILE SEQRES 8 A 312 GLU LEU ARG ASP THR ILE ALA LYS GLU TYR ASP VAL ASN SEQRES 9 A 312 ASN LEU LEU ILE ASN ILE GLY GLY ASP HIS SER ILE GLY SEQRES 10 A 312 LEU GLY THR ILE ALA GLY VAL VAL LYS ALA MET LYS PRO SEQRES 11 A 312 ASN ALA ARG VAL GLY VAL VAL TRP PHE ASP ALA HIS PRO SEQRES 12 A 312 ASP MET ASN THR PRO GLU ASN SER PRO SER GLY ASN ILE SEQRES 13 A 312 HIS GLY MET PRO LEU ALA CYS ALA VAL GLY LEU GLY PRO SEQRES 14 A 312 GLN ARG LEU THR SER ILE MET PRO HIS TYR ILE THR PRO SEQRES 15 A 312 LYS ASP ILE MET TYR VAL GLY ILE ARG SER ILE ASP VAL SEQRES 16 A 312 GLY GLU GLN PHE GLU ILE GLN ASP LYS HIS ILE ASP HIS SEQRES 17 A 312 PHE THR ALA GLU ASP VAL LYS ARG VAL GLY MET LYS GLU SEQRES 18 A 312 VAL ILE GLU ALA ILE ASN LYS LYS PHE VAL ASP TYR ASP SEQRES 19 A 312 VAL ILE HIS LEU SER PHE ASP ILE ASP GLY ILE ASP PRO SEQRES 20 A 312 GLU PHE ILE LEU GLY THR GLY THR PRO VAL PRO LYS GLY SEQRES 21 A 312 ILE SER LEU GLU ASP SER LEU TYR PHE MET SER GLU MET SEQRES 22 A 312 GLY LYS MET LYS LYS LEU HIS SER VAL ASP ILE VAL GLU SEQRES 23 A 312 TYR ASN PRO LYS ILE GLU GLU GLU ILE THR GLY LYS ASN SEQRES 24 A 312 VAL LEU LYS CYS ILE SER SER LEU PHE GLY ILE LYS CYS SEQRES 1 B 312 HIS HIS HIS HIS HIS HIS SER SER GLY GLU ASN LEU TYR SEQRES 2 B 312 PHE GLN SER MET GLN PHE GLU LYS VAL THR TYR ILE ALA SEQRES 3 B 312 VAL PRO GLN LYS TYR GLY GLN LYS LYS VAL GLY VAL GLU SEQRES 4 B 312 GLU GLY PRO LYS PHE LEU GLU LYS LEU GLY PHE MET ASN SEQRES 5 B 312 VAL LEU GLU GLN VAL ALA LYS SER VAL ASN LYS LYS THR SEQRES 6 B 312 ILE THR GLU PRO LYS THR PRO GLN GLU LEU GLY VAL THR SEQRES 7 B 312 ASN ALA ARG ASN LEU ASN GLU VAL GLU SER VAL ASN ILE SEQRES 8 B 312 GLU LEU ARG ASP THR ILE ALA LYS GLU TYR ASP VAL ASN SEQRES 9 B 312 ASN LEU LEU ILE ASN ILE GLY GLY ASP HIS SER ILE GLY SEQRES 10 B 312 LEU GLY THR ILE ALA GLY VAL VAL LYS ALA MET LYS PRO SEQRES 11 B 312 ASN ALA ARG VAL GLY VAL VAL TRP PHE ASP ALA HIS PRO SEQRES 12 B 312 ASP MET ASN THR PRO GLU ASN SER PRO SER GLY ASN ILE SEQRES 13 B 312 HIS GLY MET PRO LEU ALA CYS ALA VAL GLY LEU GLY PRO SEQRES 14 B 312 GLN ARG LEU THR SER ILE MET PRO HIS TYR ILE THR PRO SEQRES 15 B 312 LYS ASP ILE MET TYR VAL GLY ILE ARG SER ILE ASP VAL SEQRES 16 B 312 GLY GLU GLN PHE GLU ILE GLN ASP LYS HIS ILE ASP HIS SEQRES 17 B 312 PHE THR ALA GLU ASP VAL LYS ARG VAL GLY MET LYS GLU SEQRES 18 B 312 VAL ILE GLU ALA ILE ASN LYS LYS PHE VAL ASP TYR ASP SEQRES 19 B 312 VAL ILE HIS LEU SER PHE ASP ILE ASP GLY ILE ASP PRO SEQRES 20 B 312 GLU PHE ILE LEU GLY THR GLY THR PRO VAL PRO LYS GLY SEQRES 21 B 312 ILE SER LEU GLU ASP SER LEU TYR PHE MET SER GLU MET SEQRES 22 B 312 GLY LYS MET LYS LYS LEU HIS SER VAL ASP ILE VAL GLU SEQRES 23 B 312 TYR ASN PRO LYS ILE GLU GLU GLU ILE THR GLY LYS ASN SEQRES 24 B 312 VAL LEU LYS CYS ILE SER SER LEU PHE GLY ILE LYS CYS HET ORN A 301 9 HET MN A 302 1 HET MN A 303 1 HET EDO A 304 4 HET ORN B 301 9 HET MN B 302 1 HET MN B 303 1 HETNAM ORN L-ORNITHINE HETNAM MN MANGANESE (II) ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ORN 2(C5 H12 N2 O2) FORMUL 4 MN 4(MN 2+) FORMUL 6 EDO C2 H6 O2 FORMUL 10 HOH *74(H2 O) HELIX 1 AA1 GLY A 21 GLU A 23 5 3 HELIX 2 AA2 GLU A 24 LEU A 32 1 9 HELIX 3 AA3 GLY A 33 GLU A 39 1 7 HELIX 4 AA4 ASN A 66 TYR A 85 1 20 HELIX 5 AA5 SER A 99 MET A 112 1 14 HELIX 6 AA6 ASN A 139 GLY A 142 5 4 HELIX 7 AA7 MET A 143 VAL A 149 1 7 HELIX 8 AA8 PRO A 153 SER A 158 1 6 HELIX 9 AA9 THR A 165 LYS A 167 5 3 HELIX 10 AB1 ASP A 178 LYS A 188 1 11 HELIX 11 AB2 ALA A 195 GLY A 202 1 8 HELIX 12 AB3 GLY A 202 PHE A 214 1 13 HELIX 13 AB4 ASP A 227 ILE A 229 5 3 HELIX 14 AB5 SER A 246 LYS A 259 1 14 HELIX 15 AB6 GLU A 277 GLY A 293 1 17 HELIX 16 AB7 GLY B 21 GLU B 23 5 3 HELIX 17 AB8 GLU B 24 LEU B 32 1 9 HELIX 18 AB9 GLY B 33 GLU B 39 1 7 HELIX 19 AC1 ASN B 66 TYR B 85 1 20 HELIX 20 AC2 SER B 99 MET B 112 1 14 HELIX 21 AC3 ASN B 139 GLY B 142 5 4 HELIX 22 AC4 MET B 143 VAL B 149 1 7 HELIX 23 AC5 PRO B 153 SER B 158 1 6 HELIX 24 AC6 THR B 165 LYS B 167 5 3 HELIX 25 AC7 ASP B 178 LYS B 188 1 11 HELIX 26 AC8 ALA B 195 GLY B 202 1 8 HELIX 27 AC9 GLY B 202 PHE B 214 1 13 HELIX 28 AD1 ASP B 227 ILE B 229 5 3 HELIX 29 AD2 SER B 246 LYS B 259 1 14 HELIX 30 AD3 GLU B 277 GLY B 293 1 17 SHEET 1 AA116 ASP A 191 THR A 194 0 SHEET 2 AA116 ILE A 169 ILE A 174 1 N TYR A 171 O PHE A 193 SHEET 3 AA116 VAL A 118 PHE A 123 1 N TRP A 122 O MET A 170 SHEET 4 AA116 VAL A 219 ASP A 225 1 O VAL A 219 N GLY A 119 SHEET 5 AA116 LEU A 263 VAL A 269 1 O ASP A 267 N LEU A 222 SHEET 6 AA116 LEU A 90 GLY A 95 1 N ASN A 93 O VAL A 266 SHEET 7 AA116 LYS A 5 VAL A 11 1 N THR A 7 O ILE A 92 SHEET 8 AA116 SER A 44 THR A 49 1 O LYS A 48 N ALA A 10 SHEET 9 AA116 SER B 44 THR B 49 -1 O VAL B 45 N LYS A 47 SHEET 10 AA116 LYS B 5 VAL B 11 1 N TYR B 8 O LYS B 48 SHEET 11 AA116 LEU B 90 GLY B 95 1 O ILE B 92 N THR B 7 SHEET 12 AA116 LEU B 263 VAL B 269 1 O VAL B 266 N ASN B 93 SHEET 13 AA116 VAL B 219 ASP B 225 1 N LEU B 222 O ASP B 267 SHEET 14 AA116 VAL B 118 PHE B 123 1 N GLY B 119 O VAL B 219 SHEET 15 AA116 ILE B 169 ILE B 174 1 O MET B 170 N TRP B 122 SHEET 16 AA116 ASP B 191 THR B 194 1 O PHE B 193 N TYR B 171 LINK ND1 HIS A 98 MN MN A 302 1555 1555 2.28 LINK OD2 ASP A 124 MN MN A 302 1555 1555 1.99 LINK OD1 ASP A 124 MN MN A 303 1555 1555 1.96 LINK ND1 HIS A 126 MN MN A 303 1555 1555 2.35 LINK OD2 ASP A 128 MN MN A 302 1555 1555 2.28 LINK OD2 ASP A 225 MN MN A 302 1555 1555 2.19 LINK OD2 ASP A 225 MN MN A 303 1555 1555 2.28 LINK OD1 ASP A 227 MN MN A 303 1555 1555 2.58 LINK OD2 ASP A 227 MN MN A 303 1555 1555 2.52 LINK MN MN A 302 O HOH A 401 1555 1555 2.31 LINK MN MN A 302 O HOH A 406 1555 1555 2.73 LINK MN MN A 303 O HOH A 401 1555 1555 2.02 LINK ND1 HIS B 98 MN MN B 302 1555 1555 2.29 LINK OD2 ASP B 124 MN MN B 302 1555 1555 1.96 LINK OD1 ASP B 124 MN MN B 303 1555 1555 2.17 LINK ND1 HIS B 126 MN MN B 303 1555 1555 2.58 LINK OD2 ASP B 128 MN MN B 302 1555 1555 2.26 LINK OD2 ASP B 225 MN MN B 302 1555 1555 2.47 LINK OD2 ASP B 225 MN MN B 303 1555 1555 2.43 LINK OD1 ASP B 227 MN MN B 303 1555 1555 2.38 LINK OD2 ASP B 227 MN MN B 303 1555 1555 2.76 LINK MN MN B 302 O HOH B 402 1555 1555 2.14 LINK MN MN B 303 O HOH B 402 1555 1555 2.06 CISPEP 1 GLY A 95 GLY A 96 0 11.43 CISPEP 2 GLN B -1 SER B 0 0 9.19 CISPEP 3 GLY B 95 GLY B 96 0 11.33 SITE 1 AC1 9 HIS A 126 ASP A 128 ASN A 130 SER A 137 SITE 2 AC1 9 HIS A 141 ASP A 178 HOH A 401 HOH A 403 SITE 3 AC1 9 HOH A 406 SITE 1 AC2 7 HIS A 98 ASP A 124 ASP A 128 ASP A 225 SITE 2 AC2 7 MN A 303 HOH A 401 HOH A 406 SITE 1 AC3 6 ASP A 124 HIS A 126 ASP A 225 ASP A 227 SITE 2 AC3 6 MN A 302 HOH A 401 SITE 1 AC4 3 ASN A 115 ARG A 117 ASP A 218 SITE 1 AC5 10 HIS B 126 ASP B 128 ASN B 130 SER B 137 SITE 2 AC5 10 HIS B 141 GLY B 142 ASP B 178 HOH B 402 SITE 3 AC5 10 HOH B 405 HOH B 412 SITE 1 AC6 6 HIS B 98 ASP B 124 ASP B 128 ASP B 225 SITE 2 AC6 6 MN B 303 HOH B 402 SITE 1 AC7 6 ASP B 124 HIS B 126 ASP B 225 ASP B 227 SITE 2 AC7 6 MN B 302 HOH B 402 CRYST1 87.605 97.494 133.255 90.00 90.00 90.00 I 21 21 21 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 0.011415 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010257 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007504 0.00000