HEADER OXIDOREDUCTASE 22-MAY-16 5K4W TITLE THREE-DIMENSIONAL STRUCTURE OF L-THREONINE 3-DEHYDROGENASE FROM TITLE 2 TRYPANOSOMA BRUCEI BOUND TO NADH AND L-THREONINE REFINED TO 1.72 TITLE 3 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, LIGAND-BOUND, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR E.A.ADJOGATSE,P.T.ERSKINE,J.B.COOPER REVDAT 3 10-OCT-18 5K4W 1 JRNL REVDAT 2 19-SEP-18 5K4W 1 JRNL REVDAT 1 10-JAN-18 5K4W 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. 1.72 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 64406 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) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3443 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) : 1.72 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4704 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE SET COUNT : 271 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5012 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 124 REMARK 3 SOLVENT ATOMS : 420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : -0.08000 REMARK 3 B33 (A**2) : 0.11000 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): 0.097 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.970 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5250 ; 0.020 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 5008 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7136 ; 2.104 ; 2.009 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11580 ; 1.094 ; 3.007 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 639 ; 6.617 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 207 ;34.642 ;23.865 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 895 ;13.554 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;17.753 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 816 ; 0.430 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5739 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1103 ; 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): 2568 ; 2.339 ; 2.454 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2568 ; 2.338 ; 2.454 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3203 ; 3.137 ; 3.668 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 5K4W 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_1000221768. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-13 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 : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67909 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 46.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.76500 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM ACETATE, 0.1M TRIS, 30% REMARK 280 W/V PEG 4000, NADH (10MM), L-THREONINE (30MM), PH 8.5, VAPOR REMARK 280 DIFFUSION, 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 41.72500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 68.06000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.72500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 68.06000 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: 5760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 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 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 1001 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 1529 O HOH C 1670 1.93 REMARK 500 ND2 ASN C 1111 O HOH C 1501 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A1075 CG TYR A1075 CD1 -0.082 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 A1023 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 PHE A1062 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 PHE A1062 CB - CG - CD1 ANGL. DEV. = 4.4 DEGREES REMARK 500 GLU A1105 CG - CD - OE1 ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG C1023 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG C1084 CD - NE - CZ ANGL. DEV. = 9.5 DEGREES REMARK 500 ARG C1084 NE - CZ - NH1 ANGL. DEV. = 10.3 DEGREES REMARK 500 ARG C1084 NE - CZ - NH2 ANGL. DEV. = -8.1 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 SER A1118 -161.86 -102.00 REMARK 500 SER C1118 -160.96 -104.17 REMARK 500 ARG C1262 115.21 -160.39 REMARK 500 SER C1320 -125.60 -101.99 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 A1404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A1210 OE2 REMARK 620 2 SER A1211 O 85.7 REMARK 620 3 ALA A1277 O 77.8 125.7 REMARK 620 4 TRP A1280 O 134.2 138.8 80.6 REMARK 620 5 ASP A1282 OD1 89.2 69.5 158.4 97.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C1405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C1210 OE2 REMARK 620 2 ALA C1277 O 83.7 REMARK 620 3 TRP C1280 O 139.3 83.6 REMARK 620 4 ASP C1282 OD1 89.5 166.7 94.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAI A 1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue THR A 1402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 1404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAI C 1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue THR C 1402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 1403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 1404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA C 1405 DBREF 5K4W A 1003 1321 UNP Q7YW97 Q7YW97_9TRYP 14 332 DBREF 5K4W C 1003 1321 UNP Q7YW97 Q7YW97_9TRYP 14 332 SEQADV 5K4W HIS A 1001 UNP Q7YW97 EXPRESSION TAG SEQADV 5K4W MET A 1002 UNP Q7YW97 EXPRESSION TAG SEQADV 5K4W HIS C 1001 UNP Q7YW97 EXPRESSION TAG SEQADV 5K4W MET C 1002 UNP Q7YW97 EXPRESSION TAG SEQRES 1 A 321 HIS MET PRO ARG VAL LEU VAL THR GLY ALA LEU GLY GLN SEQRES 2 A 321 ILE GLY THR ASP LEU SER LEU ALA LEU ARG ASP LYS PHE SEQRES 3 A 321 GLY ALA ASP SER VAL LEU VAL SER ASP VAL VAL GLU PRO SEQRES 4 A 321 GLY ALA LYS HIS PRO LEU ALA GLY LEU LYS GLY VAL GLU SEQRES 5 A 321 LYS LEU ASP CYS LEU ASP SER ASN GLY PHE GLU LYS LEU SEQRES 6 A 321 VAL LYS GLU PHE LYS PRO THR TRP MET TYR HIS LEU PRO SEQRES 7 A 321 ALA ILE MET SER VAL ARG GLY GLU ALA GLU PRO ASP LEU SEQRES 8 A 321 ALA MET ASP ILE ASN VAL ASN THR THR ARG TYR ALA LEU SEQRES 9 A 321 GLU LEU ALA ARG LYS TYR ASN ILE ARG ILE PHE ILE PRO SEQRES 10 A 321 SER THR ILE ALA ALA PHE GLY ASP LYS CYS GLY LYS THR SEQRES 11 A 321 MET THR LYS ASP ASP THR ILE MET ASN PRO SER THR VAL SEQRES 12 A 321 TYR GLY VAL THR LYS VAL TYR THR GLU LEU LEU GLY THR SEQRES 13 A 321 TRP TYR ARG GLN LYS TYR GLY VAL ASP PHE ARG SER VAL SEQRES 14 A 321 ARG LEU PRO GLY ILE ILE SER ALA ALA THR LEU PRO GLY SEQRES 15 A 321 GLY GLY ALA THR ASP TYR ALA ILE HIS MET TYR HIS SER SEQRES 16 A 321 ALA LEU LEU GLN LYS LYS CYS VAL CYS PRO VAL LEU PRO SEQRES 17 A 321 TYR GLU SER LEU PRO MET MET TYR MET PRO ASP THR LEU SEQRES 18 A 321 ASN SER LEU VAL LYS ILE MET GLU ALA PRO LEU GLU LYS SEQRES 19 A 321 LEU THR ARG THR VAL TYR ASN ILE THR GLY PHE SER PHE SEQRES 20 A 321 SER PRO SER GLU LEU ARG PHE SER ILE GLU ARG CYS THR SEQRES 21 A 321 ASP ARG THR ILE GLU VAL GLU TYR VAL GLU GLY PRO ALA SEQRES 22 A 321 GLN LYS ILE ALA ASN SER TRP PRO ASP SER LEU ASP ASP SEQRES 23 A 321 SER ASN ALA ARG ASN ASP TRP GLY HIS GLN VAL LYS TYR SEQRES 24 A 321 ASP ILE ASP MET MET SER GLU ASP MET LEU ARG GLN ILE SEQRES 25 A 321 PRO ILE LEU HIS GLY LEU PRO SER LEU SEQRES 1 C 321 HIS MET PRO ARG VAL LEU VAL THR GLY ALA LEU GLY GLN SEQRES 2 C 321 ILE GLY THR ASP LEU SER LEU ALA LEU ARG ASP LYS PHE SEQRES 3 C 321 GLY ALA ASP SER VAL LEU VAL SER ASP VAL VAL GLU PRO SEQRES 4 C 321 GLY ALA LYS HIS PRO LEU ALA GLY LEU LYS GLY VAL GLU SEQRES 5 C 321 LYS LEU ASP CYS LEU ASP SER ASN GLY PHE GLU LYS LEU SEQRES 6 C 321 VAL LYS GLU PHE LYS PRO THR TRP MET TYR HIS LEU PRO SEQRES 7 C 321 ALA ILE MET SER VAL ARG GLY GLU ALA GLU PRO ASP LEU SEQRES 8 C 321 ALA MET ASP ILE ASN VAL ASN THR THR ARG TYR ALA LEU SEQRES 9 C 321 GLU LEU ALA ARG LYS TYR ASN ILE ARG ILE PHE ILE PRO SEQRES 10 C 321 SER THR ILE ALA ALA PHE GLY ASP LYS CYS GLY LYS THR SEQRES 11 C 321 MET THR LYS ASP ASP THR ILE MET ASN PRO SER THR VAL SEQRES 12 C 321 TYR GLY VAL THR LYS VAL TYR THR GLU LEU LEU GLY THR SEQRES 13 C 321 TRP TYR ARG GLN LYS TYR GLY VAL ASP PHE ARG SER VAL SEQRES 14 C 321 ARG LEU PRO GLY ILE ILE SER ALA ALA THR LEU PRO GLY SEQRES 15 C 321 GLY GLY ALA THR ASP TYR ALA ILE HIS MET TYR HIS SER SEQRES 16 C 321 ALA LEU LEU GLN LYS LYS CYS VAL CYS PRO VAL LEU PRO SEQRES 17 C 321 TYR GLU SER LEU PRO MET MET TYR MET PRO ASP THR LEU SEQRES 18 C 321 ASN SER LEU VAL LYS ILE MET GLU ALA PRO LEU GLU LYS SEQRES 19 C 321 LEU THR ARG THR VAL TYR ASN ILE THR GLY PHE SER PHE SEQRES 20 C 321 SER PRO SER GLU LEU ARG PHE SER ILE GLU ARG CYS THR SEQRES 21 C 321 ASP ARG THR ILE GLU VAL GLU TYR VAL GLU GLY PRO ALA SEQRES 22 C 321 GLN LYS ILE ALA ASN SER TRP PRO ASP SER LEU ASP ASP SEQRES 23 C 321 SER ASN ALA ARG ASN ASP TRP GLY HIS GLN VAL LYS TYR SEQRES 24 C 321 ASP ILE ASP MET MET SER GLU ASP MET LEU ARG GLN ILE SEQRES 25 C 321 PRO ILE LEU HIS GLY LEU PRO SER LEU HET NAI A1401 44 HET THR A1402 8 HET GOL A1403 6 HET NA A1404 1 HET NAI C1401 44 HET THR C1402 8 HET GOL C1403 6 HET GOL C1404 6 HET NA C1405 1 HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE HETNAM THR THREONINE HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN NAI NADH HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NAI 2(C21 H29 N7 O14 P2) FORMUL 4 THR 2(C4 H9 N O3) FORMUL 5 GOL 3(C3 H8 O3) FORMUL 6 NA 2(NA 1+) FORMUL 12 HOH *420(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 TYR A 1110 1 23 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 GLY A 1184 THR A 1186 5 3 HELIX 8 AA8 ASP A 1187 GLN A 1199 1 13 HELIX 9 AA9 MET A 1217 ALA A 1230 1 14 HELIX 10 AB1 PRO A 1231 LEU A 1235 5 5 HELIX 11 AB2 SER A 1248 ASP A 1261 1 14 HELIX 12 AB3 GLY A 1271 SER A 1279 1 9 HELIX 13 AB4 ASP A 1286 GLY A 1294 1 9 HELIX 14 AB5 ASP A 1300 GLY A 1317 1 18 HELIX 15 AB6 GLY C 1012 GLY C 1027 1 16 HELIX 16 AB7 ASP C 1058 LYS C 1070 1 13 HELIX 17 AB8 MET C 1081 GLU C 1088 1 8 HELIX 18 AB9 GLU C 1088 ASN C 1111 1 24 HELIX 19 AC1 ALA C 1121 PHE C 1123 5 3 HELIX 20 AC2 THR C 1142 GLY C 1163 1 22 HELIX 21 AC3 GLY C 1184 THR C 1186 5 3 HELIX 22 AC4 ASP C 1187 GLN C 1199 1 13 HELIX 23 AC5 MET C 1217 ALA C 1230 1 14 HELIX 24 AC6 PRO C 1231 LEU C 1235 5 5 HELIX 25 AC7 SER C 1248 ASP C 1261 1 14 HELIX 26 AC8 GLY C 1271 TRP C 1280 1 10 HELIX 27 AC9 ASP C 1286 GLY C 1294 1 9 HELIX 28 AD1 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 TYR C1075 N THR C1008 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 TYR C1075 N THR C1008 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 C1245 N MET C1214 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 OE2 GLU A1210 NA NA A1404 1555 1555 2.84 LINK O SER A1211 NA NA A1404 1555 1555 3.07 LINK O ALA A1277 NA NA A1404 1555 1555 2.95 LINK O TRP A1280 NA NA A1404 1555 1555 2.76 LINK OD1 ASP A1282 NA NA A1404 1555 1555 2.94 LINK OE2 GLU C1210 NA NA C1405 1555 1555 2.85 LINK O ALA C1277 NA NA C1405 1555 1555 2.89 LINK O TRP C1280 NA NA C1405 1555 1555 2.72 LINK OD1 ASP C1282 NA NA C1405 1555 1555 3.12 SITE 1 AC1 33 GLY A1009 LEU A1011 GLY A1012 GLN A1013 SITE 2 AC1 33 ILE A1014 ASP A1035 VAL A1036 LEU A1054 SITE 3 AC1 33 ASP A1055 CYS A1056 LEU A1077 PRO A1078 SITE 4 AC1 33 ALA A1079 MET A1081 ILE A1095 PRO A1117 SITE 5 AC1 33 SER A1118 TYR A1144 LYS A1148 LEU A1171 SITE 6 AC1 33 PRO A1172 ILE A1174 GLY A1182 THR A1402 SITE 7 AC1 33 HOH A1510 HOH A1514 HOH A1526 HOH A1561 SITE 8 AC1 33 HOH A1563 HOH A1585 HOH A1605 HOH A1624 SITE 9 AC1 33 HOH A1675 SITE 1 AC2 10 MET A1081 SER A1082 THR A1119 TYR A1144 SITE 2 AC2 10 GLY A1184 ALA A1185 THR A1186 TRP A1280 SITE 3 AC2 10 NAI A1401 HOH A1534 SITE 1 AC3 5 ASP A1017 SER A1176 ALA A1177 ALA A1178 SITE 2 AC3 5 TYR A1216 SITE 1 AC4 7 GLU A1210 SER A1211 LEU A1212 ALA A1277 SITE 2 AC4 7 TRP A1280 PRO A1281 ASP A1282 SITE 1 AC5 32 GLY C1009 LEU C1011 GLY C1012 GLN C1013 SITE 2 AC5 32 ILE C1014 ASP C1035 VAL C1036 LEU C1054 SITE 3 AC5 32 ASP C1055 CYS C1056 LEU C1077 PRO C1078 SITE 4 AC5 32 ALA C1079 MET C1081 ILE C1095 PRO C1117 SITE 5 AC5 32 SER C1118 TYR C1144 LYS C1148 LEU C1171 SITE 6 AC5 32 PRO C1172 ILE C1174 GLY C1182 THR C1402 SITE 7 AC5 32 HOH C1516 HOH C1517 HOH C1526 HOH C1533 SITE 8 AC5 32 HOH C1539 HOH C1557 HOH C1559 HOH C1614 SITE 1 AC6 10 MET C1081 SER C1082 THR C1119 TYR C1144 SITE 2 AC6 10 GLY C1184 ALA C1185 THR C1186 TRP C1280 SITE 3 AC6 10 NAI C1401 HOH C1518 SITE 1 AC7 5 ASP C1017 SER C1176 ALA C1177 ALA C1178 SITE 2 AC7 5 TYR C1216 SITE 1 AC8 5 ARG C1023 ASP C1024 LYS C1025 GLY C1027 SITE 2 AC8 5 HOH C1567 SITE 1 AC9 8 LYS C1129 GLU C1210 SER C1211 LEU C1212 SITE 2 AC9 8 ALA C1277 TRP C1280 PRO C1281 ASP C1282 CRYST1 83.450 136.120 55.690 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 0.011983 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007346 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017957 0.00000