HEADER ISOMERASE 17-OCT-18 6ILB TITLE NATIVE CRYSTAL STRUCTURE OF FRUCTURONATE-TAGATURONATE EPIMERASE UXAE TITLE 2 FROM COHNELLA LAEVIRIBOSI COMPND MOL_ID: 1; COMPND 2 MOLECULE: FRUCTURONATE-TAGATURONATE EPIMERASE UXAE; COMPND 3 CHAIN: A, D; COMPND 4 EC: 5.1.2.7; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: COHNELLA LAEVIRIBOSI; SOURCE 3 ORGANISM_TAXID: 380174; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET29A KEYWDS UXAE, TIM-BARREL, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.Y.CHOI,L.W.KANG,T.H.HO,D.Q.NGUYEN,I.H.LEE,J.H.LEE,Y.S.PARK,H.J.PARK REVDAT 1 23-OCT-19 6ILB 0 JRNL AUTH M.Y.CHOI,L.W.KANG,T.H.HO,D.Q.NGUYEN,I.H.LEE,J.H.LEE, JRNL AUTH 2 Y.S.PARK,H.J.PARK JRNL TITL CRYSTAL STRUCTURE OF FRUCTURONATE-TAGATURONATE EPIMERASE JRNL TITL 2 UXAE FROM COHNELLA LAEVIRIBOSI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.51 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 31632 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1681 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) : 2.51 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2117 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE SET COUNT : 94 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7784 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 40 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : -0.02000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 2.519 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.334 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.246 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.985 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7950 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 7312 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10728 ; 1.564 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16894 ; 1.018 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 976 ; 6.474 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 406 ;35.183 ;23.448 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1362 ;17.404 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 66 ;20.662 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1154 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8964 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1718 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6ILB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009404. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97940 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33313 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 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) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.40700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD 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 (%): 48.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MGCL2, 15% (W/V) PEG 3350, 0.1 M REMARK 280 TRIS (BASE)/HCL (PH 8.5), EVAPORATION, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 A 4 CG CD OE1 NE2 REMARK 470 GLN D 4 CG CD OE1 NE2 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 LYS A 2 34.15 -98.62 REMARK 500 GLU A 26 -127.12 64.41 REMARK 500 GLU A 36 128.96 -15.67 REMARK 500 ALA A 58 105.99 -166.66 REMARK 500 ASP A 59 -112.33 56.32 REMARK 500 GLN A 89 61.95 -108.64 REMARK 500 LEU A 95 79.78 -116.46 REMARK 500 ALA A 193 147.52 -30.21 REMARK 500 SER A 196 -35.91 70.94 REMARK 500 ASP A 219 27.77 47.91 REMARK 500 GLU A 273 72.49 -101.38 REMARK 500 ALA A 367 -78.32 -164.54 REMARK 500 THR A 407 44.38 -104.79 REMARK 500 LEU D 10 -73.35 -65.56 REMARK 500 GLU D 26 -127.71 59.85 REMARK 500 ALA D 58 136.85 152.00 REMARK 500 ASP D 59 -145.40 67.78 REMARK 500 GLN D 89 62.98 -109.78 REMARK 500 LEU D 95 76.59 -118.50 REMARK 500 ALA D 190 -44.60 166.36 REMARK 500 SER D 196 -48.35 -171.25 REMARK 500 ASP D 219 26.72 41.93 REMARK 500 ALA D 367 -75.93 -159.62 REMARK 500 ALA D 447 121.72 -31.43 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 ALA A 35 GLU A 36 -142.22 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 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 160 NE2 REMARK 620 2 SER A 270 OG 89.4 REMARK 620 3 ASP A 272 OD1 163.9 77.6 REMARK 620 4 HIS A 342 ND1 89.3 91.0 100.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 160 NE2 REMARK 620 2 SER D 270 OG 86.9 REMARK 620 3 ASP D 272 OD1 160.6 73.8 REMARK 620 4 GLU D 273 OE1 90.6 74.7 82.4 REMARK 620 5 HIS D 342 ND1 89.1 91.0 93.3 165.8 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 MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN D 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO D 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide GLY D 344 and SEP D REMARK 800 345 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide SEP D 345 and ASP D REMARK 800 346 REMARK 999 REMARK 999 SEQUENCE REMARK 999 WP_019005805.1 FOR SEQUENCE REFERENCE DBREF 6ILB A 1 489 PDB 6ILB 6ILB 1 489 DBREF 6ILB D 1 489 PDB 6ILB 6ILB 1 489 SEQRES 1 A 489 MET LYS ALA GLN SER ILE ILE GLU ARG LEU ALA ALA GLY SEQRES 2 A 489 GLN VAL HIS VAL TYR PRO ARG SER ARG HIS GLU SER GLU SEQRES 3 A 489 GLY THR ARG VAL GLN MET ILE LYS ALA GLU GLY ARG LYS SEQRES 4 A 489 TYR LEU VAL ALA GLU GLY SER GLY LYS LEU TYR ASP GLU SEQRES 5 A 489 LEU ARG GLY GLU GLU ALA ASP GLY VAL LYS LEU CYS GLU SEQRES 6 A 489 LEU SER HIS GLU ASN ARG LEU VAL LEU ASN ARG HIS PHE SEQRES 7 A 489 PRO PHE THR VAL PRO GLN ALA PHE GLY LYS GLN SER ALA SEQRES 8 A 489 THR ILE GLY LEU GLY ASP ARG LEU GLY ILE ALA GLY PRO SEQRES 9 A 489 GLY HIS VAL GLN THR VAL ARG GLY ARG ALA ILE HIS PRO SEQRES 10 A 489 ILE LEU ALA GLN GLN SER ILE ARG GLU LEU ALA LEU THR SEQRES 11 A 489 GLY ARG ASP TYR LYS GLN VAL ILE ASP ALA ALA ALA TYR SEQRES 12 A 489 ALA VAL PHE GLN GLU GLY TYR THR GLU GLY TYR GLY ALA SEQRES 13 A 489 ASP GLY ASP HIS LEU LYS LYS GLU GLU ASP ILE ARG MET SEQRES 14 A 489 ALA LEU ASP LEU GLY PHE THR MET LEU THR LEU ASP CYS SEQRES 15 A 489 SER GLU GLN ILE ASP ASN GLU ALA ALA GLN ALA GLY GLU SEQRES 16 A 489 SER GLU VAL LYS ARG LYS TYR GLU GLU LEU PRO GLU SER SEQRES 17 A 489 VAL ARG SER HIS TYR GLU ALA LYS TYR LEU ASP LYS THR SEQRES 18 A 489 PHE GLN VAL GLY PRO HIS ALA ILE HIS PHE ASP ALA ALA SEQRES 19 A 489 THR LEU MET ARG ASP VAL LEU VAL TYR ARG GLU ALA ILE SEQRES 20 A 489 GLN PHE MET ILE TYR ILE TYR GLU LYS TYR ILE GLN THR SEQRES 21 A 489 ALA GLY ARG ALA VAL ASP PHE GLU ILE SER ILE ASP GLU SEQRES 22 A 489 THR LEU THR PRO THR ALA PRO GLY SER HIS PHE LEU VAL SEQRES 23 A 489 ALA SER GLU LEU ILE GLY LYS ASN VAL ASP ILE PHE SER SEQRES 24 A 489 MET ALA PRO ARG PHE ILE GLY GLU PHE GLN LYS GLY ILE SEQRES 25 A 489 ASP TYR ILE GLY ASP ILE ALA GLN PHE GLU ARG GLU LEU SEQRES 26 A 489 ALA VAL HIS ALA ALA ILE ALA ASP ARG PHE GLY TYR LYS SEQRES 27 A 489 LEU SER ILE HIS SER GLY SEP ASP LYS PHE SER VAL PHE SEQRES 28 A 489 ALA LEU VAL GLY ARG TYR THR ASN GLY ARG PHE HIS VAL SEQRES 29 A 489 LYS THR ALA GLY THR ASN TRP LEU GLU ALA VAL ARG ILE SEQRES 30 A 489 VAL ALA LYS THR ASN PRO GLY LEU TYR ARG ARG MET HIS SEQRES 31 A 489 GLN TYR ALA LEU GLU HIS PHE GLU GLU ALA THR ALA TYR SEQRES 32 A 489 TYR HIS VAL THR THR ASN LEU ASN ASN ILE ARG PRO LEU SEQRES 33 A 489 ALA ASP VAL SER ASP GLU GLU LEU PRO SER TYR MET ASN SEQRES 34 A 489 GLU ASN ASP ALA ARG GLN LEU LEU HIS ILE THR TYR GLY SEQRES 35 A 489 LEU LEU LEU GLN ALA LYS LYS ASP ASP GLY SER SER LEU SEQRES 36 A 489 PHE ARG ASP GLU PHE PHE ARG THR LEU SER GLU ARG GLU SEQRES 37 A 489 GLU ASP TYR GLU ALA ALA LEU ARG SER HIS ILE GLY LYS SEQRES 38 A 489 HIS LEU ASP LEU LEU GLY VAL LYS SEQRES 1 D 489 MET LYS ALA GLN SER ILE ILE GLU ARG LEU ALA ALA GLY SEQRES 2 D 489 GLN VAL HIS VAL TYR PRO ARG SER ARG HIS GLU SER GLU SEQRES 3 D 489 GLY THR ARG VAL GLN MET ILE LYS ALA GLU GLY ARG LYS SEQRES 4 D 489 TYR LEU VAL ALA GLU GLY SER GLY LYS LEU TYR ASP GLU SEQRES 5 D 489 LEU ARG GLY GLU GLU ALA ASP GLY VAL LYS LEU CYS GLU SEQRES 6 D 489 LEU SER HIS GLU ASN ARG LEU VAL LEU ASN ARG HIS PHE SEQRES 7 D 489 PRO PHE THR VAL PRO GLN ALA PHE GLY LYS GLN SER ALA SEQRES 8 D 489 THR ILE GLY LEU GLY ASP ARG LEU GLY ILE ALA GLY PRO SEQRES 9 D 489 GLY HIS VAL GLN THR VAL ARG GLY ARG ALA ILE HIS PRO SEQRES 10 D 489 ILE LEU ALA GLN GLN SER ILE ARG GLU LEU ALA LEU THR SEQRES 11 D 489 GLY ARG ASP TYR LYS GLN VAL ILE ASP ALA ALA ALA TYR SEQRES 12 D 489 ALA VAL PHE GLN GLU GLY TYR THR GLU GLY TYR GLY ALA SEQRES 13 D 489 ASP GLY ASP HIS LEU LYS LYS GLU GLU ASP ILE ARG MET SEQRES 14 D 489 ALA LEU ASP LEU GLY PHE THR MET LEU THR LEU ASP CYS SEQRES 15 D 489 SER GLU GLN ILE ASP ASN GLU ALA ALA GLN ALA GLY GLU SEQRES 16 D 489 SER GLU VAL LYS ARG LYS TYR GLU GLU LEU PRO GLU SER SEQRES 17 D 489 VAL ARG SER HIS TYR GLU ALA LYS TYR LEU ASP LYS THR SEQRES 18 D 489 PHE GLN VAL GLY PRO HIS ALA ILE HIS PHE ASP ALA ALA SEQRES 19 D 489 THR LEU MET ARG ASP VAL LEU VAL TYR ARG GLU ALA ILE SEQRES 20 D 489 GLN PHE MET ILE TYR ILE TYR GLU LYS TYR ILE GLN THR SEQRES 21 D 489 ALA GLY ARG ALA VAL ASP PHE GLU ILE SER ILE ASP GLU SEQRES 22 D 489 THR LEU THR PRO THR ALA PRO GLY SER HIS PHE LEU VAL SEQRES 23 D 489 ALA SER GLU LEU ILE GLY LYS ASN VAL ASP ILE PHE SER SEQRES 24 D 489 MET ALA PRO ARG PHE ILE GLY GLU PHE GLN LYS GLY ILE SEQRES 25 D 489 ASP TYR ILE GLY ASP ILE ALA GLN PHE GLU ARG GLU LEU SEQRES 26 D 489 ALA VAL HIS ALA ALA ILE ALA ASP ARG PHE GLY TYR LYS SEQRES 27 D 489 LEU SER ILE HIS SER GLY SEP ASP LYS PHE SER VAL PHE SEQRES 28 D 489 ALA LEU VAL GLY ARG TYR THR ASN GLY ARG PHE HIS VAL SEQRES 29 D 489 LYS THR ALA GLY THR ASN TRP LEU GLU ALA VAL ARG ILE SEQRES 30 D 489 VAL ALA LYS THR ASN PRO GLY LEU TYR ARG ARG MET HIS SEQRES 31 D 489 GLN TYR ALA LEU GLU HIS PHE GLU GLU ALA THR ALA TYR SEQRES 32 D 489 TYR HIS VAL THR THR ASN LEU ASN ASN ILE ARG PRO LEU SEQRES 33 D 489 ALA ASP VAL SER ASP GLU GLU LEU PRO SER TYR MET ASN SEQRES 34 D 489 GLU ASN ASP ALA ARG GLN LEU LEU HIS ILE THR TYR GLY SEQRES 35 D 489 LEU LEU LEU GLN ALA LYS LYS ASP ASP GLY SER SER LEU SEQRES 36 D 489 PHE ARG ASP GLU PHE PHE ARG THR LEU SER GLU ARG GLU SEQRES 37 D 489 GLU ASP TYR GLU ALA ALA LEU ARG SER HIS ILE GLY LYS SEQRES 38 D 489 HIS LEU ASP LEU LEU GLY VAL LYS HET SEP A 345 10 HET SEP D 345 10 HET MN A 501 1 HET EDO A 502 4 HET MN D 501 1 HET EDO D 502 4 HETNAM SEP PHOSPHOSERINE HETNAM MN MANGANESE (II) ION HETNAM EDO 1,2-ETHANEDIOL HETSYN SEP PHOSPHONOSERINE HETSYN EDO ETHYLENE GLYCOL FORMUL 1 SEP 2(C3 H8 N O6 P) FORMUL 3 MN 2(MN 2+) FORMUL 4 EDO 2(C2 H6 O2) FORMUL 7 HOH *40(H2 O) HELIX 1 AA1 LYS A 2 GLY A 13 1 12 HELIX 2 AA2 TYR A 18 ARG A 22 5 5 HELIX 3 AA3 GLY A 47 LEU A 53 1 7 HELIX 4 AA4 SER A 67 PHE A 78 1 12 HELIX 5 AA5 PRO A 79 VAL A 82 5 4 HELIX 6 AA6 ALA A 102 ARG A 111 1 10 HELIX 7 AA7 ILE A 124 GLY A 131 1 8 HELIX 8 AA8 ASP A 133 GLY A 149 1 17 HELIX 9 AA9 LYS A 163 LEU A 173 1 11 HELIX 10 AB1 ASP A 187 ALA A 193 1 7 HELIX 11 AB2 SER A 196 GLU A 204 1 9 HELIX 12 AB3 PRO A 206 LEU A 218 1 13 HELIX 13 AB4 ASP A 232 ILE A 258 1 27 HELIX 14 AB5 GLN A 259 GLY A 262 5 4 HELIX 15 AB6 ALA A 279 LYS A 293 1 15 HELIX 16 AB7 ASP A 317 GLY A 336 1 20 HELIX 17 AB8 VAL A 350 THR A 358 1 9 HELIX 18 AB9 ALA A 367 ASN A 382 1 16 HELIX 19 AC1 ASN A 382 THR A 401 1 20 HELIX 20 AC2 ASN A 409 ILE A 413 5 5 HELIX 21 AC3 PRO A 415 VAL A 419 5 5 HELIX 22 AC4 GLU A 423 ASN A 429 5 7 HELIX 23 AC5 GLU A 430 THR A 440 1 11 HELIX 24 AC6 THR A 440 ALA A 447 1 8 HELIX 25 AC7 PHE A 456 ARG A 467 1 12 HELIX 26 AC8 ARG A 467 GLY A 487 1 21 HELIX 27 AC9 LYS D 2 GLY D 13 1 12 HELIX 28 AD1 GLY D 47 LEU D 53 1 7 HELIX 29 AD2 SER D 67 PHE D 78 1 12 HELIX 30 AD3 PRO D 79 VAL D 82 5 4 HELIX 31 AD4 ALA D 102 ARG D 111 1 10 HELIX 32 AD5 ILE D 124 GLY D 131 1 8 HELIX 33 AD6 ASP D 133 GLY D 149 1 17 HELIX 34 AD7 LYS D 163 LEU D 173 1 11 HELIX 35 AD8 ASP D 187 GLN D 192 1 6 HELIX 36 AD9 SER D 196 LEU D 205 1 10 HELIX 37 AE1 PRO D 206 LEU D 218 1 13 HELIX 38 AE2 ASP D 232 ILE D 258 1 27 HELIX 39 AE3 ALA D 279 LYS D 293 1 15 HELIX 40 AE4 ASP D 317 GLY D 336 1 20 HELIX 41 AE5 LYS D 347 THR D 358 1 12 HELIX 42 AE6 ALA D 367 ASN D 382 1 16 HELIX 43 AE7 ASN D 382 THR D 401 1 20 HELIX 44 AE8 ASN D 409 ILE D 413 5 5 HELIX 45 AE9 PRO D 415 VAL D 419 5 5 HELIX 46 AF1 SER D 420 ASN D 429 5 10 HELIX 47 AF2 GLU D 430 THR D 440 1 11 HELIX 48 AF3 THR D 440 ALA D 447 1 8 HELIX 49 AF4 PHE D 456 ARG D 467 1 12 HELIX 50 AF5 ARG D 467 GLY D 487 1 21 SHEET 1 AA1 5 HIS A 23 SER A 25 0 SHEET 2 AA1 5 THR A 28 LYS A 34 -1 O VAL A 30 N HIS A 23 SHEET 3 AA1 5 LYS A 39 GLU A 44 -1 O VAL A 42 N GLN A 31 SHEET 4 AA1 5 VAL A 61 GLU A 65 -1 O CYS A 64 N LEU A 41 SHEET 5 AA1 5 GLU A 56 ALA A 58 -1 N GLU A 56 O LEU A 63 SHEET 1 AA2 9 THR A 92 LEU A 95 0 SHEET 2 AA2 9 HIS A 116 SER A 123 1 O ILE A 118 N ILE A 93 SHEET 3 AA2 9 GLY A 155 LEU A 161 1 O ASP A 157 N ALA A 120 SHEET 4 AA2 9 MET A 177 LEU A 180 1 O THR A 179 N GLY A 158 SHEET 5 AA2 9 ASP A 266 ILE A 271 1 O GLU A 268 N LEU A 180 SHEET 6 AA2 9 ILE A 297 PRO A 302 1 O PHE A 298 N PHE A 267 SHEET 7 AA2 9 LYS A 338 ILE A 341 1 O LYS A 338 N PHE A 298 SHEET 8 AA2 9 PHE A 362 THR A 366 1 O LYS A 365 N ILE A 341 SHEET 9 AA2 9 THR A 92 LEU A 95 1 N GLY A 94 O VAL A 364 SHEET 1 AA3 2 THR A 221 GLN A 223 0 SHEET 2 AA3 2 ALA A 228 HIS A 230 -1 O ILE A 229 N PHE A 222 SHEET 1 AA4 3 HIS D 16 VAL D 17 0 SHEET 2 AA4 3 THR D 28 ALA D 35 -1 O LYS D 34 N HIS D 16 SHEET 3 AA4 3 HIS D 23 SER D 25 -1 N HIS D 23 O VAL D 30 SHEET 1 AA5 4 HIS D 16 VAL D 17 0 SHEET 2 AA5 4 THR D 28 ALA D 35 -1 O LYS D 34 N HIS D 16 SHEET 3 AA5 4 ARG D 38 GLU D 44 -1 O VAL D 42 N GLN D 31 SHEET 4 AA5 4 VAL D 61 GLU D 65 -1 O CYS D 64 N LEU D 41 SHEET 1 AA6 9 THR D 92 LEU D 95 0 SHEET 2 AA6 9 HIS D 116 SER D 123 1 O ILE D 118 N ILE D 93 SHEET 3 AA6 9 GLY D 155 LEU D 161 1 O ASP D 157 N ALA D 120 SHEET 4 AA6 9 MET D 177 ASP D 181 1 O THR D 179 N GLY D 158 SHEET 5 AA6 9 ASP D 266 SER D 270 1 O GLU D 268 N LEU D 180 SHEET 6 AA6 9 SER D 299 ALA D 301 1 O ALA D 301 N ILE D 269 SHEET 7 AA6 9 LYS D 338 ILE D 341 1 O SER D 340 N MET D 300 SHEET 8 AA6 9 PHE D 362 THR D 366 1 O HIS D 363 N LEU D 339 SHEET 9 AA6 9 THR D 92 LEU D 95 1 N GLY D 94 O VAL D 364 SHEET 1 AA7 2 THR D 221 VAL D 224 0 SHEET 2 AA7 2 HIS D 227 HIS D 230 -1 O HIS D 227 N VAL D 224 LINK NE2 HIS A 160 MN MN A 501 1555 1555 2.34 LINK OG SER A 270 MN MN A 501 1555 1555 2.27 LINK OD1 ASP A 272 MN MN A 501 1555 1555 1.89 LINK ND1 HIS A 342 MN MN A 501 1555 1555 2.42 LINK C GLY A 344 N SEP A 345 1555 1555 1.32 LINK C SEP A 345 N ASP A 346 1555 1555 1.33 LINK NE2 HIS D 160 MN MN D 501 1555 1555 2.31 LINK OG SER D 270 MN MN D 501 1555 1555 2.30 LINK OD1 ASP D 272 MN MN D 501 1555 1555 1.93 LINK OE1 GLU D 273 MN MN D 501 1555 1555 2.34 LINK ND1 HIS D 342 MN MN D 501 1555 1555 2.31 LINK C GLY D 344 N SEP D 345 1555 1555 1.32 LINK C SEP D 345 N ASP D 346 1555 1555 1.33 SITE 1 AC1 5 HIS A 160 SER A 270 ASP A 272 GLU A 273 SITE 2 AC1 5 HIS A 342 SITE 1 AC2 7 LYS A 310 HIS A 342 SER A 343 SEP A 345 SITE 2 AC2 7 LYS A 365 THR A 366 ALA A 367 SITE 1 AC3 5 HIS D 160 SER D 270 ASP D 272 GLU D 273 SITE 2 AC3 5 HIS D 342 SITE 1 AC4 4 ASP D 159 HIS D 160 SER D 343 SEP D 345 SITE 1 AC5 12 HIS D 342 SER D 343 ASP D 346 LYS D 347 SITE 2 AC5 12 PHE D 351 LYS D 365 THR D 366 ALA D 367 SITE 3 AC5 12 GLY D 368 THR D 369 HIS D 438 EDO D 502 SITE 1 AC6 16 GLY D 311 ASP D 313 SER D 343 GLY D 344 SITE 2 AC6 16 LYS D 347 PHE D 348 LYS D 365 THR D 366 SITE 3 AC6 16 ALA D 367 GLY D 368 THR D 369 ARG D 434 SITE 4 AC6 16 HIS D 438 HIS D 478 HIS D 482 EDO D 502 CRYST1 51.816 73.470 74.673 98.14 110.16 90.12 P 1 2 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 0.019299 0.000040 0.007173 0.00000 SCALE2 0.000000 0.013611 0.002086 0.00000 SCALE3 0.000000 0.000000 0.014432 0.00000