HEADER LYASE 14-NOV-02 1N7H TITLE CRYSTAL STRUCTURE OF GDP-MANNOSE 4,6-DEHYDRATASE TERNARY COMPLEX WITH TITLE 2 NADPH AND GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: GDP-D-MANNOSE-4,6-DEHYDRATASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 4.2.1.47; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: MUR1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS ROSSMANN FOLD, SDR, SHORT-CHAIN DEHYDROGENASE/REDUCTASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR A.M.MULICHAK,C.P.BONIN,W.-D.REITER,R.M.GARAVITO REVDAT 3 13-JUL-11 1N7H 1 VERSN REVDAT 2 24-FEB-09 1N7H 1 VERSN REVDAT 1 07-JAN-03 1N7H 0 JRNL AUTH A.M.MULICHAK,C.P.BONIN,W.-D.REITER,R.M.GARAVITO JRNL TITL THE STRUCTURE OF THE MUR1 GDP-MANNOSE 4,6-DEHYDRATASE FROM JRNL TITL 2 A. THALIANA: IMPLICATIONS FOR LIGAND BINDING AND JRNL TITL 3 SPECIFICITY. JRNL REF BIOCHEMISTRY V. 41 15578 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12501186 JRNL DOI 10.1021/BI0266683 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 69991 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 SET) : 0.181 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3557 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1900 REMARK 3 BIN FREE R VALUE : 0.2150 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 312 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5240 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 152 REMARK 3 SOLVENT ATOMS : 440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.38 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.14 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.02 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 PARTIAL OR NO SIDE CHAIN ATOMS WERE REFINED FOR RESIDUES LISTED REMARK 3 IN REMARK 470. REMARK 4 REMARK 4 1N7H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-NOV-02. REMARK 100 THE RCSB ID CODE IS RCSB017614. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS - B4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70104 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.07700 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PEG 400, IMIDAZOLE REMARK 280 BUFFER, PH 6.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 55.24500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.24500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 58.43000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.22000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 58.43000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 62.22000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 55.24500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 58.43000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 62.22000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 55.24500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 58.43000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 62.22000 REMARK 290 SMTRY3 8 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A TETRAMER GENERATED FROM THE REMARK 300 DIMER IN THE ASYMMETRIC UNIT BY THE TRANSFORMATION: -X+1, Y, -Z+1/2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 20910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 116.86000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 55.24500 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 792 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 675 LIES ON A SPECIAL POSITION. 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 GLU A 4 REMARK 465 ASN A 5 REMARK 465 ASN A 6 REMARK 465 GLY A 7 REMARK 465 SER A 8 REMARK 465 ARG A 9 REMARK 465 SER A 10 REMARK 465 ASP A 11 REMARK 465 SER A 12 REMARK 465 GLU A 13 REMARK 465 SER A 14 REMARK 465 ILE A 15 REMARK 465 THR A 16 REMARK 465 ALA A 17 REMARK 465 PRO A 18 REMARK 465 LYS A 19 REMARK 465 ALA A 20 REMARK 465 ASP A 21 REMARK 465 SER A 22 REMARK 465 THR A 23 REMARK 465 VAL A 24 REMARK 465 VAL A 25 REMARK 465 GLU A 26 REMARK 465 PRO A 27 REMARK 465 ILE A 75 REMARK 465 ASP A 76 REMARK 465 PRO A 77 REMARK 465 HIS A 78 REMARK 465 ASN A 79 REMARK 465 VAL A 80 REMARK 465 ASN A 81 REMARK 465 LYS A 82 REMARK 465 MET A 367 REMARK 465 ASP A 368 REMARK 465 ALA A 369 REMARK 465 LYS A 370 REMARK 465 GLN A 371 REMARK 465 GLN A 372 REMARK 465 PRO A 373 REMARK 465 LEU A 374 REMARK 465 GLU A 375 REMARK 465 HIS A 376 REMARK 465 HIS A 377 REMARK 465 HIS A 378 REMARK 465 HIS A 379 REMARK 465 HIS A 380 REMARK 465 HIS A 381 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 GLU B 4 REMARK 465 ASN B 5 REMARK 465 ASN B 6 REMARK 465 GLY B 7 REMARK 465 SER B 8 REMARK 465 ARG B 9 REMARK 465 SER B 10 REMARK 465 ASP B 11 REMARK 465 SER B 12 REMARK 465 GLU B 13 REMARK 465 SER B 14 REMARK 465 ILE B 15 REMARK 465 THR B 16 REMARK 465 ALA B 17 REMARK 465 PRO B 18 REMARK 465 LYS B 19 REMARK 465 ALA B 20 REMARK 465 ASP B 21 REMARK 465 SER B 22 REMARK 465 THR B 23 REMARK 465 VAL B 24 REMARK 465 VAL B 25 REMARK 465 GLU B 26 REMARK 465 PRO B 27 REMARK 465 ASP B 76 REMARK 465 PRO B 77 REMARK 465 HIS B 78 REMARK 465 ASN B 79 REMARK 465 VAL B 80 REMARK 465 ASN B 81 REMARK 465 ASP B 368 REMARK 465 ALA B 369 REMARK 465 LYS B 370 REMARK 465 GLN B 371 REMARK 465 GLN B 372 REMARK 465 PRO B 373 REMARK 465 LEU B 374 REMARK 465 GLU B 375 REMARK 465 HIS B 376 REMARK 465 HIS B 377 REMARK 465 HIS B 378 REMARK 465 HIS B 379 REMARK 465 HIS B 380 REMARK 465 HIS B 381 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 LYS A 86 CG CD CE NZ REMARK 470 LYS A 273 CD CE NZ REMARK 470 GLU A 283 CG CD OE1 OE2 REMARK 470 GLU A 330 CG CD OE1 OE2 REMARK 470 LYS A 335 CG CD CE NZ REMARK 470 GLN A 337 CD OE1 NE2 REMARK 470 LYS A 342 CD CE NZ REMARK 470 LYS A 359 CD CE NZ REMARK 470 PHE B 65 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ILE B 75 CG1 CG2 CD1 REMARK 470 LYS B 82 CG CD CE NZ REMARK 470 LYS B 86 CD CE NZ REMARK 470 LYS B 106 CD CE NZ REMARK 470 LYS B 243 CD CE NZ REMARK 470 LYS B 273 CD CE NZ REMARK 470 ARG B 311 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 329 CG CD CE NZ REMARK 470 GLU B 330 CG CD OE1 OE2 REMARK 470 LYS B 335 CG CD CE NZ REMARK 470 GLN B 337 CD OE1 NE2 REMARK 470 GLU B 341 CG CD OE1 OE2 REMARK 470 LYS B 342 CD CE NZ 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 O HOH B 872 O HOH B 872 3655 1.86 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 GLN A 116 N - CA - C ANGL. DEV. = -19.9 DEGREES REMARK 500 ARG A 145 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 GLN B 116 N - CA - C ANGL. DEV. = -20.5 DEGREES REMARK 500 ARG B 145 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 145 NE - CZ - NH2 ANGL. DEV. = -3.9 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 ALA A 134 -68.62 -97.28 REMARK 500 SER A 217 176.70 177.69 REMARK 500 ALA A 364 2.99 -64.73 REMARK 500 ALA B 134 -67.91 -97.74 REMARK 500 SER B 217 176.39 178.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 GLN A 116 45.4 L L OUTSIDE RANGE REMARK 500 GLN B 116 45.6 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP B 702 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1N7G RELATED DB: PDB DBREF 1N7H A 1 373 UNP P93031 GMD2_ARATH 1 373 DBREF 1N7H B 1 373 UNP P93031 GMD2_ARATH 1 373 SEQADV 1N7H LEU A 374 UNP P93031 EXPRESSION TAG SEQADV 1N7H GLU A 375 UNP P93031 EXPRESSION TAG SEQADV 1N7H HIS A 376 UNP P93031 EXPRESSION TAG SEQADV 1N7H HIS A 377 UNP P93031 EXPRESSION TAG SEQADV 1N7H HIS A 378 UNP P93031 EXPRESSION TAG SEQADV 1N7H HIS A 379 UNP P93031 EXPRESSION TAG SEQADV 1N7H HIS A 380 UNP P93031 EXPRESSION TAG SEQADV 1N7H HIS A 381 UNP P93031 EXPRESSION TAG SEQADV 1N7H LEU B 374 UNP P93031 EXPRESSION TAG SEQADV 1N7H GLU B 375 UNP P93031 EXPRESSION TAG SEQADV 1N7H HIS B 376 UNP P93031 EXPRESSION TAG SEQADV 1N7H HIS B 377 UNP P93031 EXPRESSION TAG SEQADV 1N7H HIS B 378 UNP P93031 EXPRESSION TAG SEQADV 1N7H HIS B 379 UNP P93031 EXPRESSION TAG SEQADV 1N7H HIS B 380 UNP P93031 EXPRESSION TAG SEQADV 1N7H HIS B 381 UNP P93031 EXPRESSION TAG SEQRES 1 A 381 MET ALA SER GLU ASN ASN GLY SER ARG SER ASP SER GLU SEQRES 2 A 381 SER ILE THR ALA PRO LYS ALA ASP SER THR VAL VAL GLU SEQRES 3 A 381 PRO ARG LYS ILE ALA LEU ILE THR GLY ILE THR GLY GLN SEQRES 4 A 381 ASP GLY SER TYR LEU THR GLU PHE LEU LEU GLY LYS GLY SEQRES 5 A 381 TYR GLU VAL HIS GLY LEU ILE ARG ARG SER SER ASN PHE SEQRES 6 A 381 ASN THR GLN ARG ILE ASN HIS ILE TYR ILE ASP PRO HIS SEQRES 7 A 381 ASN VAL ASN LYS ALA LEU MET LYS LEU HIS TYR ALA ASP SEQRES 8 A 381 LEU THR ASP ALA SER SER LEU ARG ARG TRP ILE ASP VAL SEQRES 9 A 381 ILE LYS PRO ASP GLU VAL TYR ASN LEU ALA ALA GLN SER SEQRES 10 A 381 HIS VAL ALA VAL SER PHE GLU ILE PRO ASP TYR THR ALA SEQRES 11 A 381 ASP VAL VAL ALA THR GLY ALA LEU ARG LEU LEU GLU ALA SEQRES 12 A 381 VAL ARG SER HIS THR ILE ASP SER GLY ARG THR VAL LYS SEQRES 13 A 381 TYR TYR GLN ALA GLY SER SER GLU MET PHE GLY SER THR SEQRES 14 A 381 PRO PRO PRO GLN SER GLU THR THR PRO PHE HIS PRO ARG SEQRES 15 A 381 SER PRO TYR ALA ALA SER LYS CYS ALA ALA HIS TRP TYR SEQRES 16 A 381 THR VAL ASN TYR ARG GLU ALA TYR GLY LEU PHE ALA CYS SEQRES 17 A 381 ASN GLY ILE LEU PHE ASN HIS GLU SER PRO ARG ARG GLY SEQRES 18 A 381 GLU ASN PHE VAL THR ARG LYS ILE THR ARG ALA LEU GLY SEQRES 19 A 381 ARG ILE LYS VAL GLY LEU GLN THR LYS LEU PHE LEU GLY SEQRES 20 A 381 ASN LEU GLN ALA SER ARG ASP TRP GLY PHE ALA GLY ASP SEQRES 21 A 381 TYR VAL GLU ALA MET TRP LEU MET LEU GLN GLN GLU LYS SEQRES 22 A 381 PRO ASP ASP TYR VAL VAL ALA THR GLU GLU GLY HIS THR SEQRES 23 A 381 VAL GLU GLU PHE LEU ASP VAL SER PHE GLY TYR LEU GLY SEQRES 24 A 381 LEU ASN TRP LYS ASP TYR VAL GLU ILE ASP GLN ARG TYR SEQRES 25 A 381 PHE ARG PRO ALA GLU VAL ASP ASN LEU GLN GLY ASP ALA SEQRES 26 A 381 SER LYS ALA LYS GLU VAL LEU GLY TRP LYS PRO GLN VAL SEQRES 27 A 381 GLY PHE GLU LYS LEU VAL LYS MET MET VAL ASP GLU ASP SEQRES 28 A 381 LEU GLU LEU ALA LYS ARG GLU LYS VAL LEU VAL ASP ALA SEQRES 29 A 381 GLY TYR MET ASP ALA LYS GLN GLN PRO LEU GLU HIS HIS SEQRES 30 A 381 HIS HIS HIS HIS SEQRES 1 B 381 MET ALA SER GLU ASN ASN GLY SER ARG SER ASP SER GLU SEQRES 2 B 381 SER ILE THR ALA PRO LYS ALA ASP SER THR VAL VAL GLU SEQRES 3 B 381 PRO ARG LYS ILE ALA LEU ILE THR GLY ILE THR GLY GLN SEQRES 4 B 381 ASP GLY SER TYR LEU THR GLU PHE LEU LEU GLY LYS GLY SEQRES 5 B 381 TYR GLU VAL HIS GLY LEU ILE ARG ARG SER SER ASN PHE SEQRES 6 B 381 ASN THR GLN ARG ILE ASN HIS ILE TYR ILE ASP PRO HIS SEQRES 7 B 381 ASN VAL ASN LYS ALA LEU MET LYS LEU HIS TYR ALA ASP SEQRES 8 B 381 LEU THR ASP ALA SER SER LEU ARG ARG TRP ILE ASP VAL SEQRES 9 B 381 ILE LYS PRO ASP GLU VAL TYR ASN LEU ALA ALA GLN SER SEQRES 10 B 381 HIS VAL ALA VAL SER PHE GLU ILE PRO ASP TYR THR ALA SEQRES 11 B 381 ASP VAL VAL ALA THR GLY ALA LEU ARG LEU LEU GLU ALA SEQRES 12 B 381 VAL ARG SER HIS THR ILE ASP SER GLY ARG THR VAL LYS SEQRES 13 B 381 TYR TYR GLN ALA GLY SER SER GLU MET PHE GLY SER THR SEQRES 14 B 381 PRO PRO PRO GLN SER GLU THR THR PRO PHE HIS PRO ARG SEQRES 15 B 381 SER PRO TYR ALA ALA SER LYS CYS ALA ALA HIS TRP TYR SEQRES 16 B 381 THR VAL ASN TYR ARG GLU ALA TYR GLY LEU PHE ALA CYS SEQRES 17 B 381 ASN GLY ILE LEU PHE ASN HIS GLU SER PRO ARG ARG GLY SEQRES 18 B 381 GLU ASN PHE VAL THR ARG LYS ILE THR ARG ALA LEU GLY SEQRES 19 B 381 ARG ILE LYS VAL GLY LEU GLN THR LYS LEU PHE LEU GLY SEQRES 20 B 381 ASN LEU GLN ALA SER ARG ASP TRP GLY PHE ALA GLY ASP SEQRES 21 B 381 TYR VAL GLU ALA MET TRP LEU MET LEU GLN GLN GLU LYS SEQRES 22 B 381 PRO ASP ASP TYR VAL VAL ALA THR GLU GLU GLY HIS THR SEQRES 23 B 381 VAL GLU GLU PHE LEU ASP VAL SER PHE GLY TYR LEU GLY SEQRES 24 B 381 LEU ASN TRP LYS ASP TYR VAL GLU ILE ASP GLN ARG TYR SEQRES 25 B 381 PHE ARG PRO ALA GLU VAL ASP ASN LEU GLN GLY ASP ALA SEQRES 26 B 381 SER LYS ALA LYS GLU VAL LEU GLY TRP LYS PRO GLN VAL SEQRES 27 B 381 GLY PHE GLU LYS LEU VAL LYS MET MET VAL ASP GLU ASP SEQRES 28 B 381 LEU GLU LEU ALA LYS ARG GLU LYS VAL LEU VAL ASP ALA SEQRES 29 B 381 GLY TYR MET ASP ALA LYS GLN GLN PRO LEU GLU HIS HIS SEQRES 30 B 381 HIS HIS HIS HIS HET NDP A 601 48 HET GDP A 602 28 HET NDP B 701 48 HET GDP B 702 28 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 3 NDP 2(C21 H30 N7 O17 P3) FORMUL 4 GDP 2(C10 H15 N5 O11 P2) FORMUL 7 HOH *440(H2 O) HELIX 1 1 GLY A 38 LYS A 51 1 14 HELIX 2 2 ASP A 94 LYS A 106 1 13 HELIX 3 3 HIS A 118 ILE A 125 1 8 HELIX 4 4 ILE A 125 ALA A 134 1 10 HELIX 5 5 ALA A 134 GLY A 152 1 19 HELIX 6 6 GLU A 164 GLY A 167 5 4 HELIX 7 7 SER A 183 GLY A 204 1 22 HELIX 8 8 PHE A 224 VAL A 238 1 15 HELIX 9 9 ALA A 258 GLN A 270 1 13 HELIX 10 10 VAL A 287 LEU A 298 1 12 HELIX 11 11 ASN A 301 ASP A 304 5 4 HELIX 12 12 GLN A 310 PHE A 313 5 4 HELIX 13 13 ALA A 325 GLY A 333 1 9 HELIX 14 14 GLY A 339 ALA A 364 1 26 HELIX 15 15 GLY B 38 LYS B 51 1 14 HELIX 16 16 ILE B 70 ILE B 75 1 6 HELIX 17 17 ASP B 94 LYS B 106 1 13 HELIX 18 18 HIS B 118 ILE B 125 1 8 HELIX 19 19 ILE B 125 ALA B 134 1 10 HELIX 20 20 ALA B 134 GLY B 152 1 19 HELIX 21 21 GLU B 164 GLY B 167 5 4 HELIX 22 22 SER B 183 GLY B 204 1 22 HELIX 23 23 PHE B 224 VAL B 238 1 15 HELIX 24 24 ALA B 258 GLN B 270 1 13 HELIX 25 25 VAL B 287 LEU B 298 1 12 HELIX 26 26 ASN B 301 ASP B 304 5 4 HELIX 27 27 GLN B 310 PHE B 313 5 4 HELIX 28 28 ALA B 325 LEU B 332 1 8 HELIX 29 29 GLY B 339 ALA B 364 1 26 SHEET 1 A 7 MET A 85 TYR A 89 0 SHEET 2 A 7 GLU A 54 ILE A 59 1 N ILE A 59 O HIS A 88 SHEET 3 A 7 ILE A 30 THR A 34 1 N ILE A 33 O HIS A 56 SHEET 4 A 7 GLU A 109 ASN A 112 1 O TYR A 111 N LEU A 32 SHEET 5 A 7 LYS A 156 SER A 162 1 O TYR A 158 N ASN A 112 SHEET 6 A 7 PHE A 206 LEU A 212 1 O PHE A 206 N TYR A 157 SHEET 7 A 7 ASP A 276 VAL A 279 1 O TYR A 277 N ILE A 211 SHEET 1 B 2 HIS A 215 GLU A 216 0 SHEET 2 B 2 GLY A 256 PHE A 257 1 O GLY A 256 N GLU A 216 SHEET 1 C 2 LEU A 244 LEU A 246 0 SHEET 2 C 2 VAL A 306 ILE A 308 1 O GLU A 307 N LEU A 244 SHEET 1 D 2 SER A 252 ASP A 254 0 SHEET 2 D 2 GLY A 284 THR A 286 -1 O HIS A 285 N ARG A 253 SHEET 1 E 7 MET B 85 TYR B 89 0 SHEET 2 E 7 GLU B 54 ILE B 59 1 N ILE B 59 O HIS B 88 SHEET 3 E 7 ILE B 30 THR B 34 1 N ILE B 33 O HIS B 56 SHEET 4 E 7 GLU B 109 ASN B 112 1 O TYR B 111 N LEU B 32 SHEET 5 E 7 LYS B 156 SER B 162 1 O TYR B 158 N ASN B 112 SHEET 6 E 7 PHE B 206 LEU B 212 1 O PHE B 206 N TYR B 157 SHEET 7 E 7 ASP B 276 VAL B 279 1 O TYR B 277 N ILE B 211 SHEET 1 F 2 HIS B 215 GLU B 216 0 SHEET 2 F 2 GLY B 256 PHE B 257 1 O GLY B 256 N GLU B 216 SHEET 1 G 2 LEU B 244 LEU B 246 0 SHEET 2 G 2 VAL B 306 ILE B 308 1 O GLU B 307 N LEU B 244 SHEET 1 H 2 SER B 252 ASP B 254 0 SHEET 2 H 2 GLY B 284 THR B 286 -1 O HIS B 285 N ARG B 253 CISPEP 1 PRO A 171 PRO A 172 0 -0.15 CISPEP 2 PRO B 171 PRO B 172 0 -0.14 SITE 1 AC1 39 GLY A 35 THR A 37 GLY A 38 GLN A 39 SITE 2 AC1 39 ASP A 40 ARG A 60 ASP A 91 LEU A 92 SITE 3 AC1 39 LEU A 113 ALA A 114 ALA A 115 SER A 117 SITE 4 AC1 39 TYR A 128 VAL A 132 ALA A 160 GLY A 161 SITE 5 AC1 39 SER A 162 TYR A 185 LYS A 189 LEU A 212 SITE 6 AC1 39 ASN A 214 HIS A 215 ARG A 220 HOH A 604 SITE 7 AC1 39 HOH A 609 HOH A 611 HOH A 612 HOH A 615 SITE 8 AC1 39 HOH A 617 HOH A 620 HOH A 624 HOH A 637 SITE 9 AC1 39 HOH A 639 HOH A 640 HOH A 643 ARG B 61 SITE 10 AC1 39 SER B 62 SER B 63 HOH B 840 SITE 1 AC2 25 HIS A 118 VAL A 119 GLU A 164 ASN A 214 SITE 2 AC2 25 ASN A 223 PHE A 224 VAL A 225 LYS A 228 SITE 3 AC2 25 LEU A 246 GLY A 247 ASN A 248 ALA A 251 SITE 4 AC2 25 ARG A 253 VAL A 287 TYR A 312 ARG A 314 SITE 5 AC2 25 GLU A 317 HOH A 621 HOH A 623 HOH A 632 SITE 6 AC2 25 HOH A 636 HOH A 641 HOH A 673 HOH A 738 SITE 7 AC2 25 HOH A 803 SITE 1 AC3 39 ARG A 61 SER A 62 SER A 63 HOH A 635 SITE 2 AC3 39 HOH A 651 GLY B 35 THR B 37 GLY B 38 SITE 3 AC3 39 GLN B 39 ASP B 40 ARG B 60 ASP B 91 SITE 4 AC3 39 LEU B 92 LEU B 113 ALA B 114 ALA B 115 SITE 5 AC3 39 SER B 117 TYR B 128 VAL B 132 ALA B 160 SITE 6 AC3 39 GLY B 161 SER B 162 TYR B 185 LYS B 189 SITE 7 AC3 39 LEU B 212 ASN B 214 HIS B 215 ARG B 220 SITE 8 AC3 39 HOH B 706 HOH B 708 HOH B 710 HOH B 714 SITE 9 AC3 39 HOH B 721 HOH B 722 HOH B 724 HOH B 726 SITE 10 AC3 39 HOH B 740 HOH B 783 HOH B 811 SITE 1 AC4 23 VAL B 119 GLU B 164 ASN B 214 ASN B 223 SITE 2 AC4 23 PHE B 224 VAL B 225 LYS B 228 LEU B 246 SITE 3 AC4 23 GLY B 247 ASN B 248 ALA B 251 ARG B 253 SITE 4 AC4 23 VAL B 287 TYR B 312 ARG B 314 GLU B 317 SITE 5 AC4 23 HOH B 720 HOH B 723 HOH B 730 HOH B 753 SITE 6 AC4 23 HOH B 770 HOH B 780 HOH B 812 CRYST1 116.860 124.440 110.490 90.00 90.00 90.00 C 2 2 21 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008557 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008036 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009051 0.00000 MASTER 481 0 4 29 26 0 33 6 0 0 0 60 END