HEADER LIGASE 14-JUL-98 2NSY TITLE CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS TITLE 2 SUBTILIS IN COMPLEX WITH NAD-ADENYLATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (NAD SYNTHETASE); COMPND 3 CHAIN: A, B; COMPND 4 EC: 6.3.5.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIGASE, AMIDOTRANSFERASE, NH3 DEPENDENT, ATP PYROPHOSPHATASE EXPDTA X-RAY DIFFRACTION AUTHOR M.RIZZI,M.BOLOGNESI,A.CODA REVDAT 6 30-AUG-23 2NSY 1 REMARK LINK REVDAT 5 04-OCT-17 2NSY 1 REMARK REVDAT 4 13-JUL-11 2NSY 1 VERSN REVDAT 3 24-FEB-09 2NSY 1 VERSN REVDAT 2 29-DEC-99 2NSY 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 13-JAN-99 2NSY 0 JRNL AUTH M.RIZZI,M.BOLOGNESI,A.CODA JRNL TITL A NOVEL DEAMIDO-NAD+-BINDING SITE REVEALED BY THE TRAPPED JRNL TITL 2 NAD-ADENYLATE INTERMEDIATE IN THE NAD+ SYNTHETASE STRUCTURE. JRNL REF STRUCTURE V. 6 1129 1998 JRNL REFN ISSN 0969-2126 JRNL PMID 9753692 JRNL DOI 10.1016/S0969-2126(98)00114-2 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.RIZZI,C.NESSI,A.MATTEVI,A.CODA,M.BOLOGNESI,A.GALIZZI REMARK 1 TITL CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM REMARK 1 TITL 2 BACILLUS SUBTILIS REMARK 1 REF EMBO J. V. 15 5125 1996 REMARK 1 REFN ISSN 0261-4189 REMARK 1 REFERENCE 2 REMARK 1 AUTH C.NESSI,A.M.ALBERTINI,M.L.SPERANZA,A.GALIZZI REMARK 1 TITL THE OUTB GENE OF BACILLUS SUBTILIS CODES FOR NAD SYNTHETASE REMARK 1 REF J.BIOL.CHEM. V. 270 6181 1995 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 111493 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4264 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 166 REMARK 3 SOLVENT ATOMS : 493 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.019 ; NULL REMARK 3 ANGLE DISTANCE (A) : 0.033 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.039 ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2NSY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008040. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (AGROVATA, ROTAVATA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 111493 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: OTHER REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: 1NSY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 42.81000 REMARK 290 SMTRY3 2 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: 10950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.0 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 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 B 501 O HOH B 539 1.89 REMARK 500 CE LYS B 34 O HOH B 843 1.96 REMARK 500 NZ LYS B 238 O HOH B 765 1.98 REMARK 500 O HOH A 479 O HOH A 804 2.10 REMARK 500 O HOH A 729 O HOH A 730 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 4 O HOH B 622 2656 1.53 REMARK 500 O HOH A 627 O HOH B 532 1655 1.60 REMARK 500 OE2 GLU B 68 O HOH A 674 1554 2.05 REMARK 500 O HOH A 420 O HOH B 781 2656 2.09 REMARK 500 NZ LYS A 250 OE1 GLU B 214 1655 2.15 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 ARG A 8 CD ARG A 8 NE 0.267 REMARK 500 GLU A 162 CD GLU A 162 OE1 0.067 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 A 8 CD - NE - CZ ANGL. DEV. = -30.8 DEGREES REMARK 500 ARG A 8 NH1 - CZ - NH2 ANGL. DEV. = 47.8 DEGREES REMARK 500 ARG A 8 NE - CZ - NH1 ANGL. DEV. = -29.4 DEGREES REMARK 500 ARG A 8 NE - CZ - NH2 ANGL. DEV. = -19.6 DEGREES REMARK 500 HIS A 11 O - C - N ANGL. DEV. = -11.2 DEGREES REMARK 500 ILE A 16 CA - C - O ANGL. DEV. = 14.1 DEGREES REMARK 500 ARG A 56 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 56 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 89 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASP A 106 CB - CG - OD1 ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG A 137 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 137 NE - CZ - NH2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ASP A 173 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A 187 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 187 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 190 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 GLU A 195 OE1 - CD - OE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 GLU A 230 OE1 - CD - OE2 ANGL. DEV. = -8.2 DEGREES REMARK 500 GLU A 236 OE1 - CD - OE2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ARG A 251 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 251 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 GLU A 256 OE1 - CD - OE2 ANGL. DEV. = -10.9 DEGREES REMARK 500 ARG A 259 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG B 56 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 56 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG B 78 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 78 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP B 106 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG B 137 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 137 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 139 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 139 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG B 187 NH1 - CZ - NH2 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG B 187 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 187 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG B 190 NE - CZ - NH1 ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG B 190 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG B 201 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ASP B 229 CB - CG - OD1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ASP B 229 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 GLU B 236 OE1 - CD - OE2 ANGL. DEV. = -8.0 DEGREES REMARK 500 ARG B 259 NE - CZ - NH2 ANGL. DEV. = -8.4 DEGREES REMARK 500 MET B 265 CG - SD - CE ANGL. DEV. = -21.5 DEGREES REMARK 500 TRP B 270 O - C - N ANGL. DEV. = 9.7 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 HIS A 11 31.42 71.13 REMARK 500 HIS B 11 34.12 70.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 137 0.07 SIDE CHAIN REMARK 500 ARG A 259 0.10 SIDE CHAIN REMARK 500 ARG B 78 0.10 SIDE CHAIN REMARK 500 ARG B 201 0.13 SIDE CHAIN REMARK 500 ARG B 251 0.13 SIDE CHAIN REMARK 500 ARG B 259 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER B 241 -11.29 REMARK 500 ASP B 268 -11.10 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 MG A 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 50 OD2 REMARK 620 2 GLU A 162 OE2 83.7 REMARK 620 3 AMP A 300 O1P 170.9 89.2 REMARK 620 4 HOH A 675 O 92.7 86.7 92.5 REMARK 620 5 POP A 863 O5 98.1 177.1 89.2 90.9 REMARK 620 6 POP A 863 O1 85.8 91.9 88.8 178.1 90.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 305 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 208 O REMARK 620 2 AMP A 300 O2P 87.6 REMARK 620 3 HOH A 676 O 88.0 171.9 REMARK 620 4 HOH A 677 O 90.3 83.7 89.5 REMARK 620 5 POP A 863 O6 178.0 90.9 93.6 90.8 REMARK 620 6 POP A 863 O3 87.8 100.4 86.2 175.4 91.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 307 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 50 OD2 REMARK 620 2 GLU B 162 OE2 83.8 REMARK 620 3 AMP B 302 O1P 172.1 88.3 REMARK 620 4 HOH B 678 O 88.7 85.1 89.7 REMARK 620 5 POP B 862 O1 87.0 95.5 94.7 175.5 REMARK 620 6 POP B 862 O5 98.3 172.4 89.4 87.6 91.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 306 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 208 O REMARK 620 2 AMP B 302 O2P 85.6 REMARK 620 3 HOH B 679 O 91.6 173.1 REMARK 620 4 HOH B 680 O 91.2 83.6 90.2 REMARK 620 5 POP B 862 O3 90.8 98.9 87.4 176.9 REMARK 620 6 POP B 862 O6 176.9 91.4 91.5 89.4 88.8 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 MG A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP B 862 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP A 863 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 309 DBREF 2NSY A 1 271 UNP P08164 NADE_BACSU 2 272 DBREF 2NSY B 1 271 UNP P08164 NADE_BACSU 2 272 SEQRES 1 A 271 SER MET GLN GLU LYS ILE MET ARG GLU LEU HIS VAL LYS SEQRES 2 A 271 PRO SER ILE ASP PRO LYS GLN GLU ILE GLU ASP ARG VAL SEQRES 3 A 271 ASN PHE LEU LYS GLN TYR VAL LYS LYS THR GLY ALA LYS SEQRES 4 A 271 GLY PHE VAL LEU GLY ILE SER GLY GLY GLN ASP SER THR SEQRES 5 A 271 LEU ALA GLY ARG LEU ALA GLN LEU ALA VAL GLU SER ILE SEQRES 6 A 271 ARG GLU GLU GLY GLY ASP ALA GLN PHE ILE ALA VAL ARG SEQRES 7 A 271 LEU PRO HIS GLY THR GLN GLN ASP GLU ASP ASP ALA GLN SEQRES 8 A 271 LEU ALA LEU LYS PHE ILE LYS PRO ASP LYS SER TRP LYS SEQRES 9 A 271 PHE ASP ILE LYS SER THR VAL SER ALA PHE SER ASP GLN SEQRES 10 A 271 TYR GLN GLN GLU THR GLY ASP GLN LEU THR ASP PHE ASN SEQRES 11 A 271 LYS GLY ASN VAL LYS ALA ARG THR ARG MET ILE ALA GLN SEQRES 12 A 271 TYR ALA ILE GLY GLY GLN GLU GLY LEU LEU VAL LEU GLY SEQRES 13 A 271 THR ASP HIS ALA ALA GLU ALA VAL THR GLY PHE PHE THR SEQRES 14 A 271 LYS TYR GLY ASP GLY GLY ALA ASP LEU LEU PRO LEU THR SEQRES 15 A 271 GLY LEU THR LYS ARG GLN GLY ARG THR LEU LEU LYS GLU SEQRES 16 A 271 LEU GLY ALA PRO GLU ARG LEU TYR LEU LYS GLU PRO THR SEQRES 17 A 271 ALA ASP LEU LEU ASP GLU LYS PRO GLN GLN SER ASP GLU SEQRES 18 A 271 THR GLU LEU GLY ILE SER TYR ASP GLU ILE ASP ASP TYR SEQRES 19 A 271 LEU GLU GLY LYS GLU VAL SER ALA LYS VAL SER GLU ALA SEQRES 20 A 271 LEU GLU LYS ARG TYR SER MET THR GLU HIS LYS ARG GLN SEQRES 21 A 271 VAL PRO ALA SER MET PHE ASP ASP TRP TRP LYS SEQRES 1 B 271 SER MET GLN GLU LYS ILE MET ARG GLU LEU HIS VAL LYS SEQRES 2 B 271 PRO SER ILE ASP PRO LYS GLN GLU ILE GLU ASP ARG VAL SEQRES 3 B 271 ASN PHE LEU LYS GLN TYR VAL LYS LYS THR GLY ALA LYS SEQRES 4 B 271 GLY PHE VAL LEU GLY ILE SER GLY GLY GLN ASP SER THR SEQRES 5 B 271 LEU ALA GLY ARG LEU ALA GLN LEU ALA VAL GLU SER ILE SEQRES 6 B 271 ARG GLU GLU GLY GLY ASP ALA GLN PHE ILE ALA VAL ARG SEQRES 7 B 271 LEU PRO HIS GLY THR GLN GLN ASP GLU ASP ASP ALA GLN SEQRES 8 B 271 LEU ALA LEU LYS PHE ILE LYS PRO ASP LYS SER TRP LYS SEQRES 9 B 271 PHE ASP ILE LYS SER THR VAL SER ALA PHE SER ASP GLN SEQRES 10 B 271 TYR GLN GLN GLU THR GLY ASP GLN LEU THR ASP PHE ASN SEQRES 11 B 271 LYS GLY ASN VAL LYS ALA ARG THR ARG MET ILE ALA GLN SEQRES 12 B 271 TYR ALA ILE GLY GLY GLN GLU GLY LEU LEU VAL LEU GLY SEQRES 13 B 271 THR ASP HIS ALA ALA GLU ALA VAL THR GLY PHE PHE THR SEQRES 14 B 271 LYS TYR GLY ASP GLY GLY ALA ASP LEU LEU PRO LEU THR SEQRES 15 B 271 GLY LEU THR LYS ARG GLN GLY ARG THR LEU LEU LYS GLU SEQRES 16 B 271 LEU GLY ALA PRO GLU ARG LEU TYR LEU LYS GLU PRO THR SEQRES 17 B 271 ALA ASP LEU LEU ASP GLU LYS PRO GLN GLN SER ASP GLU SEQRES 18 B 271 THR GLU LEU GLY ILE SER TYR ASP GLU ILE ASP ASP TYR SEQRES 19 B 271 LEU GLU GLY LYS GLU VAL SER ALA LYS VAL SER GLU ALA SEQRES 20 B 271 LEU GLU LYS ARG TYR SER MET THR GLU HIS LYS ARG GLN SEQRES 21 B 271 VAL PRO ALA SER MET PHE ASP ASP TRP TRP LYS HET MG A 304 1 HET MG A 305 1 HET AMP A 300 23 HET NAD A 301 43 HET POP A 863 9 HET GOL A 308 6 HET MG B 306 1 HET MG B 307 1 HET AMP B 302 23 HET NAD B 303 43 HET POP B 862 9 HET GOL B 309 6 HETNAM MG MAGNESIUM ION HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM POP PYROPHOSPHATE 2- HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MG 4(MG 2+) FORMUL 5 AMP 2(C10 H14 N5 O7 P) FORMUL 6 NAD 2(C21 H27 N7 O14 P2) FORMUL 7 POP 2(H2 O7 P2 2-) FORMUL 8 GOL 2(C3 H8 O3) FORMUL 15 HOH *493(H2 O) HELIX 1 1 MET A 2 LEU A 10 1 9 HELIX 2 2 PRO A 18 THR A 36 1 19 HELIX 3 3 GLN A 49 GLU A 68 1 20 HELIX 4 4 GLU A 87 ILE A 97 1 11 HELIX 5 5 LYS A 108 THR A 122 1 15 HELIX 6 6 ASP A 128 GLU A 150 1 23 HELIX 7 7 ALA A 160 ALA A 163 1 4 HELIX 8 8 LYS A 186 LEU A 196 1 11 HELIX 9 9 GLU A 200 LEU A 204 1 5 HELIX 10 10 ASP A 220 LEU A 224 1 5 HELIX 11 11 TYR A 228 LEU A 235 1 8 HELIX 12 12 ALA A 242 ARG A 259 1 18 HELIX 13 13 MET B 2 GLU B 9 1 8 HELIX 14 14 PRO B 18 THR B 36 1 19 HELIX 15 15 GLN B 49 GLU B 67 1 19 HELIX 16 16 GLU B 87 ILE B 97 1 11 HELIX 17 17 LYS B 108 THR B 122 1 15 HELIX 18 18 ASP B 128 GLU B 150 1 23 HELIX 19 19 ALA B 160 ALA B 163 1 4 HELIX 20 20 LYS B 186 GLU B 195 1 10 HELIX 21 21 GLU B 200 TYR B 203 1 4 HELIX 22 22 ASP B 220 LEU B 224 1 5 HELIX 23 23 TYR B 228 LEU B 235 1 8 HELIX 24 24 ALA B 242 ARG B 259 1 18 SHEET 1 A 3 GLY A 40 GLY A 44 0 SHEET 2 A 3 GLN A 73 ARG A 78 1 N GLN A 73 O PHE A 41 SHEET 3 A 3 LYS A 101 LYS A 104 1 N LYS A 101 O ALA A 76 SHEET 1 B 3 GLY B 40 GLY B 44 0 SHEET 2 B 3 GLN B 73 ARG B 78 1 N GLN B 73 O PHE B 41 SHEET 3 B 3 LYS B 101 LYS B 104 1 N LYS B 101 O ALA B 76 LINK O3P AMP A 300 C7N NAD A 301 1555 1555 1.36 LINK O3P AMP B 302 C7N NAD B 303 1555 1555 1.37 LINK OD2 ASP A 50 MG MG A 304 1555 1555 2.09 LINK OE2 GLU A 162 MG MG A 304 1555 1555 2.10 LINK O THR A 208 MG MG A 305 1555 1555 2.10 LINK O1P AMP A 300 MG MG A 304 1555 1555 2.05 LINK O2P AMP A 300 MG MG A 305 1555 1555 2.01 LINK MG MG A 304 O HOH A 675 1555 1555 2.05 LINK MG MG A 304 O5 POP A 863 1555 1555 2.10 LINK MG MG A 304 O1 POP A 863 1555 1555 2.09 LINK MG MG A 305 O HOH A 676 1555 1555 2.10 LINK MG MG A 305 O HOH A 677 1555 1555 2.11 LINK MG MG A 305 O6 POP A 863 1555 1555 2.07 LINK MG MG A 305 O3 POP A 863 1555 1555 2.06 LINK OD2 ASP B 50 MG MG B 307 1555 1555 2.16 LINK OE2 GLU B 162 MG MG B 307 1555 1555 2.10 LINK O THR B 208 MG MG B 306 1555 1555 2.01 LINK O2P AMP B 302 MG MG B 306 1555 1555 2.07 LINK O1P AMP B 302 MG MG B 307 1555 1555 2.06 LINK MG MG B 306 O HOH B 679 1555 1555 2.08 LINK MG MG B 306 O HOH B 680 1555 1555 2.11 LINK MG MG B 306 O3 POP B 862 1555 1555 2.12 LINK MG MG B 306 O6 POP B 862 1555 1555 2.11 LINK MG MG B 307 O HOH B 678 1555 1555 2.14 LINK MG MG B 307 O1 POP B 862 1555 1555 2.04 LINK MG MG B 307 O5 POP B 862 1555 1555 2.14 SITE 1 AC1 5 ASP A 50 GLU A 162 AMP A 300 HOH A 675 SITE 2 AC1 5 POP A 863 SITE 1 AC2 5 THR A 208 AMP A 300 HOH A 676 HOH A 677 SITE 2 AC2 5 POP A 863 SITE 1 AC3 5 THR B 208 AMP B 302 HOH B 679 HOH B 680 SITE 2 AC3 5 POP B 862 SITE 1 AC4 5 ASP B 50 GLU B 162 AMP B 302 HOH B 678 SITE 2 AC4 5 POP B 862 SITE 1 AC5 24 LEU A 43 GLY A 44 ILE A 45 SER A 46 SITE 2 AC5 24 SER A 51 ARG A 78 LEU A 79 GLN A 84 SITE 3 AC5 24 ARG A 139 THR A 157 GLU A 162 ASP A 173 SITE 4 AC5 24 THR A 208 ALA A 209 NAD A 301 MG A 304 SITE 5 AC5 24 MG A 305 HOH A 331 HOH A 350 HOH A 382 SITE 6 AC5 24 HOH A 569 HOH A 675 HOH A 677 POP A 863 SITE 1 AC6 29 PHE A 129 ASN A 133 ARG A 137 PHE A 167 SITE 2 AC6 29 PHE A 168 THR A 169 LYS A 170 ASP A 173 SITE 3 AC6 29 ALA A 209 LEU A 211 GLU A 223 HIS A 257 SITE 4 AC6 29 LYS A 258 AMP A 300 HOH A 349 HOH A 389 SITE 5 AC6 29 HOH A 433 HOH A 448 HOH A 540 HOH A 569 SITE 6 AC6 29 HOH A 595 HOH A 835 TYR B 32 THR B 36 SITE 7 AC6 29 TYR B 144 LEU B 153 ASP B 177 HOH B 347 SITE 8 AC6 29 HOH B 468 SITE 1 AC7 25 LEU B 43 GLY B 44 ILE B 45 SER B 46 SITE 2 AC7 25 SER B 51 ARG B 78 LEU B 79 GLN B 84 SITE 3 AC7 25 ARG B 139 THR B 157 GLU B 162 ASP B 173 SITE 4 AC7 25 THR B 208 ALA B 209 NAD B 303 MG B 306 SITE 5 AC7 25 MG B 307 HOH B 339 HOH B 403 HOH B 486 SITE 6 AC7 25 HOH B 544 HOH B 586 HOH B 678 HOH B 680 SITE 7 AC7 25 POP B 862 SITE 1 AC8 30 TYR A 32 THR A 36 TYR A 144 LEU A 153 SITE 2 AC8 30 ASP A 177 HOH A 424 HOH A 585 ASN B 133 SITE 3 AC8 30 ARG B 137 PHE B 167 PHE B 168 THR B 169 SITE 4 AC8 30 LYS B 170 ASP B 173 ALA B 209 LEU B 211 SITE 5 AC8 30 GLU B 223 HIS B 257 LYS B 258 AMP B 302 SITE 6 AC8 30 HOH B 418 HOH B 486 HOH B 499 HOH B 520 SITE 7 AC8 30 HOH B 530 HOH B 579 HOH B 586 HOH B 648 SITE 8 AC8 30 HOH B 811 HOH B 850 SITE 1 AC9 17 SER B 46 GLY B 48 GLN B 49 ASP B 50 SITE 2 AC9 17 SER B 51 GLU B 162 LYS B 186 PRO B 207 SITE 3 AC9 17 THR B 208 AMP B 302 MG B 306 MG B 307 SITE 4 AC9 17 HOH B 359 HOH B 486 HOH B 678 HOH B 679 SITE 5 AC9 17 HOH B 680 SITE 1 BC1 17 SER A 46 GLY A 48 GLN A 49 ASP A 50 SITE 2 BC1 17 SER A 51 GLU A 162 LYS A 186 PRO A 207 SITE 3 BC1 17 THR A 208 AMP A 300 MG A 304 MG A 305 SITE 4 BC1 17 HOH A 311 HOH A 349 HOH A 675 HOH A 676 SITE 5 BC1 17 HOH A 677 SITE 1 BC2 8 ASP A 158 ALA A 163 PHE A 168 LYS A 258 SITE 2 BC2 8 ARG A 259 HOH A 800 HOH A 801 PRO B 262 SITE 1 BC3 7 PRO A 262 GLY B 174 LYS B 258 HOH B 332 SITE 2 BC3 7 HOH B 463 HOH B 607 HOH B 799 CRYST1 52.480 85.620 60.120 90.00 110.76 90.00 P 1 21 1 4 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 0.019055 0.000000 0.007223 0.00000 SCALE2 0.000000 0.011679 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017788 0.00000 MTRIX1 1 -0.608590 0.725280 -0.321830 -21.79377 1 MTRIX2 1 0.732980 0.358540 -0.578090 52.84933 1 MTRIX3 1 -0.303890 -0.587720 -0.749830 96.14252 1