HEADER OXIDOREDUCTASE 22-MAY-16 5K4V TITLE THREE-DIMENSIONAL STRUCTURE OF L-THREONINE 3-DEHYDROGENASE FROM TITLE 2 TRYPANOSOMA BRUCEI BOUND TO NAD+ REFINED TO 2.2 ANGSTROMS COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-THREONINE 3-DEHYDROGENASE; COMPND 3 CHAIN: A, C; COMPND 4 EC: 1.1.1.103; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 3 ORGANISM_TAXID: 5691; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SHORT-CHAIN DEHYDROGENASE, THREONINE, HOLO, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR E.A.ADJOGATSE,P.T.ERSKINE,J.B.COOPER REVDAT 3 10-OCT-18 5K4V 1 JRNL REVDAT 2 19-SEP-18 5K4V 1 JRNL REVDAT 1 15-NOV-17 5K4V 0 JRNL AUTH E.ADJOGATSE,P.ERSKINE,S.A.WELLS,J.M.KELLY,J.D.WILDEN, JRNL AUTH 2 A.W.E.CHAN,D.SELWOOD,A.COKER,S.WOOD,J.B.COOPER JRNL TITL STRUCTURE AND FUNCTION OF L-THREONINE-3-DEHYDROGENASE FROM JRNL TITL 2 THE PARASITIC PROTOZOAN TRYPANOSOMA BRUCEI REVEALED BY X-RAY JRNL TITL 3 CRYSTALLOGRAPHY AND GEOMETRIC SIMULATIONS. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 74 861 2018 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 30198897 JRNL DOI 10.1107/S2059798318009208 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 30829 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1642 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2277 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE SET COUNT : 90 REMARK 3 BIN FREE R VALUE : 0.2990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5002 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 170 REMARK 3 SOLVENT ATOMS : 215 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.05000 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): 0.282 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.214 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.135 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.266 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5274 ; 0.016 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 5034 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7152 ; 1.792 ; 2.015 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11578 ; 0.901 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 638 ; 7.265 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 206 ;35.696 ;23.883 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 894 ;15.981 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;17.428 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 814 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5752 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1086 ; 0.001 ; 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): 2566 ; 2.152 ; 2.713 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2557 ; 2.139 ; 2.703 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3194 ; 3.138 ; 4.042 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: NULL REMARK 4 REMARK 4 5K4V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221766. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-12 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 : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9173 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32475 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 28.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.30500 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP, PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRI-SODIUM CITRATE, 30% W/V PEG REMARK 280 4K, 0.2M SODIUM ACETATE, NAD+ (10MM), PH 8.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 45.19950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 65.76500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 45.19950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 65.76500 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 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 A 1606 O HOH A 1615 2.08 REMARK 500 NH1 ARG A 1258 O HOH A 1502 2.16 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 ARG A1084 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A1237 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG C1023 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG C1084 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG C1084 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP C1125 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 LEU C1321 CA - CB - CG ANGL. DEV. = 13.9 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 SER A1118 -157.60 -94.12 REMARK 500 SER A1320 -134.63 -77.46 REMARK 500 SER C1118 -155.16 -106.52 REMARK 500 PRO C1172 -170.00 -76.44 REMARK 500 ASP C1261 45.81 36.22 REMARK 500 GLU C1270 125.02 -39.64 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 NA A1411 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A1187 OD1 REMARK 620 2 HOH A1523 O 107.4 REMARK 620 3 HOH A1540 O 94.7 106.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C1409 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C1187 OD1 REMARK 620 2 HOH C1525 O 114.0 REMARK 620 3 HOH C1530 O 109.8 105.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 1402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 1403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 1404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 1405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 1406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 1407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 1411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD C 1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT C 1402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT C 1403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 1404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 1405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 1406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 1407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 1408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA C 1409 DBREF 5K4V A 1003 1321 UNP Q7YW97 Q7YW97_9TRYP 14 332 DBREF 5K4V C 1003 1321 UNP Q7YW97 Q7YW97_9TRYP 14 332 SEQADV 5K4V MET A 1002 UNP Q7YW97 INITIATING METHIONINE SEQADV 5K4V MET C 1002 UNP Q7YW97 INITIATING METHIONINE SEQRES 1 A 320 MET PRO ARG VAL LEU VAL THR GLY ALA LEU GLY GLN ILE SEQRES 2 A 320 GLY THR ASP LEU SER LEU ALA LEU ARG ASP LYS PHE GLY SEQRES 3 A 320 ALA ASP SER VAL LEU VAL SER ASP VAL VAL GLU PRO GLY SEQRES 4 A 320 ALA LYS HIS PRO LEU ALA GLY LEU LYS GLY VAL GLU LYS SEQRES 5 A 320 LEU ASP CYS LEU ASP SER ASN GLY PHE GLU LYS LEU VAL SEQRES 6 A 320 LYS GLU PHE LYS PRO THR TRP MET TYR HIS LEU PRO ALA SEQRES 7 A 320 ILE MET SER VAL ARG GLY GLU ALA GLU PRO ASP LEU ALA SEQRES 8 A 320 MET ASP ILE ASN VAL ASN THR THR ARG TYR ALA LEU GLU SEQRES 9 A 320 LEU ALA ARG LYS TYR ASN ILE ARG ILE PHE ILE PRO SER SEQRES 10 A 320 THR ILE ALA ALA PHE GLY ASP LYS CYS GLY LYS THR MET SEQRES 11 A 320 THR LYS ASP ASP THR ILE MET ASN PRO SER THR VAL TYR SEQRES 12 A 320 GLY VAL THR LYS VAL TYR THR GLU LEU LEU GLY THR TRP SEQRES 13 A 320 TYR ARG GLN LYS TYR GLY VAL ASP PHE ARG SER VAL ARG SEQRES 14 A 320 LEU PRO GLY ILE ILE SER ALA ALA THR LEU PRO GLY GLY SEQRES 15 A 320 GLY ALA THR ASP TYR ALA ILE HIS MET TYR HIS SER ALA SEQRES 16 A 320 LEU LEU GLN LYS LYS CYS VAL CYS PRO VAL LEU PRO TYR SEQRES 17 A 320 GLU SER LEU PRO MET MET TYR MET PRO ASP THR LEU ASN SEQRES 18 A 320 SER LEU VAL LYS ILE MET GLU ALA PRO LEU GLU LYS LEU SEQRES 19 A 320 THR ARG THR VAL TYR ASN ILE THR GLY PHE SER PHE SER SEQRES 20 A 320 PRO SER GLU LEU ARG PHE SER ILE GLU ARG CYS THR ASP SEQRES 21 A 320 ARG THR ILE GLU VAL GLU TYR VAL GLU GLY PRO ALA GLN SEQRES 22 A 320 LYS ILE ALA ASN SER TRP PRO ASP SER LEU ASP ASP SER SEQRES 23 A 320 ASN ALA ARG ASN ASP TRP GLY HIS GLN VAL LYS TYR ASP SEQRES 24 A 320 ILE ASP MET MET SER GLU ASP MET LEU ARG GLN ILE PRO SEQRES 25 A 320 ILE LEU HIS GLY LEU PRO SER LEU SEQRES 1 C 320 MET PRO ARG VAL LEU VAL THR GLY ALA LEU GLY GLN ILE SEQRES 2 C 320 GLY THR ASP LEU SER LEU ALA LEU ARG ASP LYS PHE GLY SEQRES 3 C 320 ALA ASP SER VAL LEU VAL SER ASP VAL VAL GLU PRO GLY SEQRES 4 C 320 ALA LYS HIS PRO LEU ALA GLY LEU LYS GLY VAL GLU LYS SEQRES 5 C 320 LEU ASP CYS LEU ASP SER ASN GLY PHE GLU LYS LEU VAL SEQRES 6 C 320 LYS GLU PHE LYS PRO THR TRP MET TYR HIS LEU PRO ALA SEQRES 7 C 320 ILE MET SER VAL ARG GLY GLU ALA GLU PRO ASP LEU ALA SEQRES 8 C 320 MET ASP ILE ASN VAL ASN THR THR ARG TYR ALA LEU GLU SEQRES 9 C 320 LEU ALA ARG LYS TYR ASN ILE ARG ILE PHE ILE PRO SER SEQRES 10 C 320 THR ILE ALA ALA PHE GLY ASP LYS CYS GLY LYS THR MET SEQRES 11 C 320 THR LYS ASP ASP THR ILE MET ASN PRO SER THR VAL TYR SEQRES 12 C 320 GLY VAL THR LYS VAL TYR THR GLU LEU LEU GLY THR TRP SEQRES 13 C 320 TYR ARG GLN LYS TYR GLY VAL ASP PHE ARG SER VAL ARG SEQRES 14 C 320 LEU PRO GLY ILE ILE SER ALA ALA THR LEU PRO GLY GLY SEQRES 15 C 320 GLY ALA THR ASP TYR ALA ILE HIS MET TYR HIS SER ALA SEQRES 16 C 320 LEU LEU GLN LYS LYS CYS VAL CYS PRO VAL LEU PRO TYR SEQRES 17 C 320 GLU SER LEU PRO MET MET TYR MET PRO ASP THR LEU ASN SEQRES 18 C 320 SER LEU VAL LYS ILE MET GLU ALA PRO LEU GLU LYS LEU SEQRES 19 C 320 THR ARG THR VAL TYR ASN ILE THR GLY PHE SER PHE SER SEQRES 20 C 320 PRO SER GLU LEU ARG PHE SER ILE GLU ARG CYS THR ASP SEQRES 21 C 320 ARG THR ILE GLU VAL GLU TYR VAL GLU GLY PRO ALA GLN SEQRES 22 C 320 LYS ILE ALA ASN SER TRP PRO ASP SER LEU ASP ASP SER SEQRES 23 C 320 ASN ALA ARG ASN ASP TRP GLY HIS GLN VAL LYS TYR ASP SEQRES 24 C 320 ILE ASP MET MET SER GLU ASP MET LEU ARG GLN ILE PRO SEQRES 25 C 320 ILE LEU HIS GLY LEU PRO SER LEU HET NAD A1401 44 HET ACT A1402 4 HET ACT A1403 4 HET ACT A1404 4 HET ACT A1405 4 HET ACT A1406 4 HET ACT A1407 4 HET GOL A1408 6 HET GOL A1409 6 HET GOL A1410 6 HET NA A1411 1 HET NAD C1401 44 HET ACT C1402 4 HET ACT C1403 4 HET GOL C1404 6 HET GOL C1405 6 HET GOL C1406 6 HET GOL C1407 6 HET GOL C1408 6 HET NA C1409 1 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 ACT 8(C2 H3 O2 1-) FORMUL 10 GOL 8(C3 H8 O3) FORMUL 13 NA 2(NA 1+) FORMUL 23 HOH *215(H2 O) HELIX 1 AA1 GLY A 1012 GLY A 1027 1 16 HELIX 2 AA2 ASP A 1058 LYS A 1070 1 13 HELIX 3 AA3 MET A 1081 GLU A 1088 1 8 HELIX 4 AA4 GLU A 1088 ASN A 1111 1 24 HELIX 5 AA5 ALA A 1121 PHE A 1123 5 3 HELIX 6 AA6 THR A 1142 GLY A 1163 1 22 HELIX 7 AA7 THR A 1186 LEU A 1198 1 13 HELIX 8 AA8 MET A 1217 ALA A 1230 1 14 HELIX 9 AA9 PRO A 1231 LEU A 1235 5 5 HELIX 10 AB1 SER A 1248 ASP A 1261 1 14 HELIX 11 AB2 GLY A 1271 TRP A 1280 1 10 HELIX 12 AB3 ASP A 1286 GLY A 1294 1 9 HELIX 13 AB4 ASP A 1300 GLY A 1317 1 18 HELIX 14 AB5 GLY C 1012 GLY C 1027 1 16 HELIX 15 AB6 ASP C 1058 LYS C 1070 1 13 HELIX 16 AB7 MET C 1081 GLU C 1088 1 8 HELIX 17 AB8 GLU C 1088 TYR C 1110 1 23 HELIX 18 AB9 ALA C 1121 PHE C 1123 5 3 HELIX 19 AC1 THR C 1142 GLY C 1163 1 22 HELIX 20 AC2 THR C 1186 GLN C 1199 1 14 HELIX 21 AC3 MET C 1217 ALA C 1230 1 14 HELIX 22 AC4 PRO C 1231 LEU C 1235 5 5 HELIX 23 AC5 SER C 1248 ASP C 1261 1 14 HELIX 24 AC6 PRO C 1272 TRP C 1280 1 9 HELIX 25 AC7 ASP C 1286 GLY C 1294 1 9 HELIX 26 AC8 ASP C 1300 GLY C 1317 1 18 SHEET 1 AA1 7 VAL A1051 LYS A1053 0 SHEET 2 AA1 7 VAL A1031 ASP A1035 1 N VAL A1033 O GLU A1052 SHEET 3 AA1 7 VAL A1005 THR A1008 1 N VAL A1005 O LEU A1032 SHEET 4 AA1 7 TRP A1073 HIS A1076 1 O TYR A1075 N LEU A1006 SHEET 5 AA1 7 ARG A1113 PHE A1115 1 O PHE A1115 N MET A1074 SHEET 6 AA1 7 PHE A1166 LEU A1171 1 O ARG A1167 N ILE A1114 SHEET 7 AA1 7 SER A1118 THR A1119 1 N SER A1118 O VAL A1169 SHEET 1 AA2 7 VAL A1051 LYS A1053 0 SHEET 2 AA2 7 VAL A1031 ASP A1035 1 N VAL A1033 O GLU A1052 SHEET 3 AA2 7 VAL A1005 THR A1008 1 N VAL A1005 O LEU A1032 SHEET 4 AA2 7 TRP A1073 HIS A1076 1 O TYR A1075 N LEU A1006 SHEET 5 AA2 7 ARG A1113 PHE A1115 1 O PHE A1115 N MET A1074 SHEET 6 AA2 7 PHE A1166 LEU A1171 1 O ARG A1167 N ILE A1114 SHEET 7 AA2 7 VAL A1239 ASN A1241 1 O TYR A1240 N ARG A1170 SHEET 1 AA3 3 GLY A1173 ILE A1175 0 SHEET 2 AA3 3 LEU A1212 TYR A1216 1 O MET A1215 N ILE A1175 SHEET 3 AA3 3 PHE A1245 PHE A1247 -1 O PHE A1245 N MET A1214 SHEET 1 AA4 2 CYS A1202 CYS A1204 0 SHEET 2 AA4 2 VAL A1266 TYR A1268 1 O GLU A1267 N CYS A1204 SHEET 1 AA5 7 VAL C1051 LYS C1053 0 SHEET 2 AA5 7 VAL C1031 ASP C1035 1 N VAL C1033 O GLU C1052 SHEET 3 AA5 7 VAL C1005 THR C1008 1 N VAL C1005 O LEU C1032 SHEET 4 AA5 7 TRP C1073 HIS C1076 1 O TRP C1073 N LEU C1006 SHEET 5 AA5 7 ARG C1113 PHE C1115 1 O PHE C1115 N MET C1074 SHEET 6 AA5 7 PHE C1166 LEU C1171 1 O ARG C1167 N ILE C1114 SHEET 7 AA5 7 SER C1118 THR C1119 1 N SER C1118 O VAL C1169 SHEET 1 AA6 7 VAL C1051 LYS C1053 0 SHEET 2 AA6 7 VAL C1031 ASP C1035 1 N VAL C1033 O GLU C1052 SHEET 3 AA6 7 VAL C1005 THR C1008 1 N VAL C1005 O LEU C1032 SHEET 4 AA6 7 TRP C1073 HIS C1076 1 O TRP C1073 N LEU C1006 SHEET 5 AA6 7 ARG C1113 PHE C1115 1 O PHE C1115 N MET C1074 SHEET 6 AA6 7 PHE C1166 LEU C1171 1 O ARG C1167 N ILE C1114 SHEET 7 AA6 7 VAL C1239 ASN C1241 1 O TYR C1240 N ARG C1170 SHEET 1 AA7 3 GLY C1173 ILE C1175 0 SHEET 2 AA7 3 LEU C1212 TYR C1216 1 O MET C1215 N ILE C1175 SHEET 3 AA7 3 PHE C1245 PHE C1247 -1 O PHE C1247 N LEU C1212 SHEET 1 AA8 2 CYS C1202 CYS C1204 0 SHEET 2 AA8 2 VAL C1266 TYR C1268 1 O GLU C1267 N CYS C1202 LINK OD1 ASP A1187 NA NA A1411 1555 1555 2.75 LINK OD1 ASP C1187 NA NA C1409 1555 1555 2.45 LINK NA NA A1411 O HOH A1523 1555 1555 2.87 LINK NA NA A1411 O HOH A1540 1555 1555 2.74 LINK NA NA C1409 O HOH C1525 1555 1555 3.02 LINK NA NA C1409 O HOH C1530 1555 1555 2.62 SITE 1 AC1 31 GLY A1009 LEU A1011 GLY A1012 GLN A1013 SITE 2 AC1 31 ILE A1014 ASP A1035 VAL A1036 LEU A1054 SITE 3 AC1 31 ASP A1055 CYS A1056 LEU A1077 PRO A1078 SITE 4 AC1 31 ALA A1079 MET A1081 ILE A1095 PRO A1117 SITE 5 AC1 31 SER A1118 TYR A1144 LYS A1148 LEU A1171 SITE 6 AC1 31 PRO A1172 ILE A1174 GLY A1182 ACT A1407 SITE 7 AC1 31 NA A1411 HOH A1504 HOH A1523 HOH A1529 SITE 8 AC1 31 HOH A1540 HOH A1541 HOH A1545 SITE 1 AC2 4 ASN A1060 GLU A1063 LYS A1067 HOH A1511 SITE 1 AC3 3 ALA A1028 ASP A1029 VAL A1031 SITE 1 AC4 3 THR A1072 ASN A1111 HOH A1547 SITE 1 AC5 3 SER A1246 GLU A1251 HOH A1575 SITE 1 AC6 4 GLU A1105 TYR A1158 TYR A1162 ASP C1090 SITE 1 AC7 5 MET A1081 SER A1082 THR A1119 TYR A1144 SITE 2 AC7 5 NAD A1401 SITE 1 AC8 6 ASP A1017 SER A1176 ALA A1177 ALA A1178 SITE 2 AC8 6 TYR A1216 GLN A1311 SITE 1 AC9 5 ARG A1159 LEU A1232 LEU A1235 THR A1236 SITE 2 AC9 5 THR A1238 SITE 1 AD1 9 TYR A1162 GLY A1163 HOH A1546 HOH A1586 SITE 2 AD1 9 LEU C1207 PRO C1208 TYR C1209 GLU C1210 SITE 3 AD1 9 ASN C1278 SITE 1 AD2 5 MET A1081 ASP A1187 NAD A1401 HOH A1523 SITE 2 AD2 5 HOH A1540 SITE 1 AD3 31 GLY C1009 LEU C1011 GLY C1012 GLN C1013 SITE 2 AD3 31 ILE C1014 ASP C1035 VAL C1036 LEU C1054 SITE 3 AD3 31 ASP C1055 CYS C1056 LEU C1077 PRO C1078 SITE 4 AD3 31 ALA C1079 MET C1081 ILE C1095 PRO C1117 SITE 5 AD3 31 SER C1118 THR C1119 TYR C1144 LYS C1148 SITE 6 AD3 31 LEU C1171 PRO C1172 ILE C1174 GLY C1182 SITE 7 AD3 31 ACT C1402 HOH C1514 HOH C1519 HOH C1525 SITE 8 AD3 31 HOH C1530 HOH C1534 HOH C1556 SITE 1 AD4 7 MET C1081 SER C1082 THR C1119 TYR C1144 SITE 2 AD4 7 TRP C1280 NAD C1401 HOH C1507 SITE 1 AD5 3 THR A1238 HOH A1559 LYS C1126 SITE 1 AD6 6 ASP C1017 ALA C1177 ALA C1178 TYR C1216 SITE 2 AD6 6 MET C1217 PRO C1218 SITE 1 AD7 7 ARG A1159 GLN A1160 LYS A1161 GLU C1270 SITE 2 AD7 7 GLN C1274 LYS C1275 ASN C1278 SITE 1 AD8 5 TYR A1268 ASP C1058 ASN C1060 GLY C1061 SITE 2 AD8 5 HOH C1546 SITE 1 AD9 5 ARG C1159 LEU C1232 LEU C1235 ARG C1237 SITE 2 AD9 5 HOH C1554 SITE 1 AE1 5 LYS C1133 ASP C1134 ASP C1135 ASN C1288 SITE 2 AE1 5 HOH C1506 SITE 1 AE2 6 GLN C1013 MET C1081 PRO C1181 ASP C1187 SITE 2 AE2 6 HOH C1525 HOH C1530 CRYST1 90.399 131.530 55.020 90.00 90.00 90.00 P 21 21 2 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 0.011062 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007603 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018175 0.00000