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 4 14-FEB-24 1N7H 1 REMARK SEQADV 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) : 1.380 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.14 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.020 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 DEPOSITION ID IS D_1000017614. 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 675 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 792 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. = -4.0 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 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