HEADER TRANSPORT PROTEIN 22-FEB-07 2EFC TITLE ARA7-GDP/ATVPS9A COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIMILARITY TO VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN COMPND 3 VPS9; COMPND 4 CHAIN: A, C; COMPND 5 FRAGMENT: VPS9 DOMAIN; COMPND 6 SYNONYM: ATVPS9A, HYPOTHETICAL PROTEIN AT3G19770; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SMALL GTP-BINDING PROTEIN-LIKE; COMPND 10 CHAIN: B, D; COMPND 11 FRAGMENT: GTPASE DOMAIN; COMPND 12 SYNONYM: ARA7, AT4G19640/F24J7_190; COMPND 13 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA-GAMI(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX4T1; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 12 ORGANISM_COMMON: THALE CRESS; SOURCE 13 ORGANISM_TAXID: 3702; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: DH5ALPHA; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PGEX4T1 KEYWDS GEF, GTPASE, VPS9, RAB5, NUCLEOTIDE, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.UEJIMA,K.IHARA,T.GOH,E.ITO,M.SUNADA,T.UEDA,A.NAKANO,S.WAKATSUKI REVDAT 6 03-APR-24 2EFC 1 REMARK REVDAT 5 13-MAR-24 2EFC 1 REMARK SEQADV REVDAT 4 21-DEC-11 2EFC 1 JRNL REVDAT 3 13-JUL-11 2EFC 1 VERSN REVDAT 2 24-FEB-09 2EFC 1 VERSN REVDAT 1 26-FEB-08 2EFC 0 JRNL AUTH T.UEJIMA,K.IHARA,T.GOH,E.ITO,M.SUNADA,T.UEDA,A.NAKANO, JRNL AUTH 2 S.WAKATSUKI JRNL TITL GDP-BOUND AND NUCLEOTIDE-FREE INTERMEDIATES OF THE GUANINE JRNL TITL 2 NUCLEOTIDE EXCHANGE IN THE RAB5/VPS9 SYSTEM JRNL REF J.BIOL.CHEM. V. 285 36689 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20833725 JRNL DOI 10.1074/JBC.M110.152132 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 45719 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2448 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.09 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2557 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE SET COUNT : 147 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6480 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 331 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.09000 REMARK 3 B22 (A**2) : -0.37000 REMARK 3 B33 (A**2) : 1.27000 REMARK 3 B12 (A**2) : 0.53000 REMARK 3 B13 (A**2) : -0.07000 REMARK 3 B23 (A**2) : -0.41000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.294 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.230 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.177 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.572 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.904 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6662 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9010 ; 1.263 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 818 ; 6.080 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 316 ;40.046 ;25.127 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1170 ;16.966 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;22.420 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1000 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5014 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3349 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4644 ; 0.301 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 416 ; 0.166 ; 0.200 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): 81 ; 0.263 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.134 ; 0.200 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): 4212 ; 0.673 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6592 ; 1.153 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2775 ; 1.573 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2418 ; 2.583 ; 4.500 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 : MASK 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2EFC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000026595. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48167 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : 0.07200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.29500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 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: NUCLEOTIDE-FREE ARA7/ATVPS9A WHICH WAS SOLVED BY REMARK 200 MAD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 200MM LITHIUM CITRATE, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 ASN A 3 REMARK 465 THR A 4 REMARK 465 ASP A 5 REMARK 465 VAL A 6 REMARK 465 PHE A 7 REMARK 465 LEU A 8 REMARK 465 GLY A 9 REMARK 465 LEU A 10 REMARK 465 HIS A 11 REMARK 465 ASP A 12 REMARK 465 PHE A 13 REMARK 465 LEU A 14 REMARK 465 GLU A 15 REMARK 465 ARG A 16 REMARK 465 ILE A 263 REMARK 465 SER A 264 REMARK 465 GLY A 265 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ALA B 3 REMARK 465 ALA B 4 REMARK 465 GLY B 5 REMARK 465 ASN B 6 REMARK 465 LYS B 7 REMARK 465 ARG B 173 REMARK 465 VAL B 174 REMARK 465 GLN B 175 REMARK 465 PRO B 176 REMARK 465 THR B 177 REMARK 465 GLU B 178 REMARK 465 ASN B 179 REMARK 465 GLY C -1 REMARK 465 SER C 0 REMARK 465 MET C 1 REMARK 465 GLU C 2 REMARK 465 ASN C 3 REMARK 465 THR C 4 REMARK 465 ASP C 5 REMARK 465 VAL C 6 REMARK 465 PHE C 7 REMARK 465 LEU C 8 REMARK 465 GLY C 9 REMARK 465 LEU C 10 REMARK 465 HIS C 11 REMARK 465 ASP C 12 REMARK 465 PHE C 13 REMARK 465 LEU C 14 REMARK 465 GLU C 15 REMARK 465 ARG C 16 REMARK 465 ILE C 263 REMARK 465 SER C 264 REMARK 465 GLY C 265 REMARK 465 GLY D -1 REMARK 465 SER D 0 REMARK 465 MET D 1 REMARK 465 ALA D 2 REMARK 465 ALA D 3 REMARK 465 ALA D 4 REMARK 465 GLY D 5 REMARK 465 ASN D 6 REMARK 465 LYS D 7 REMARK 465 ARG D 173 REMARK 465 VAL D 174 REMARK 465 GLN D 175 REMARK 465 PRO D 176 REMARK 465 THR D 177 REMARK 465 GLU D 178 REMARK 465 ASN D 179 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 OE2 GLU B 107 O HOH B 1202 1.92 REMARK 500 CD GLU B 107 O HOH B 1202 2.04 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 96 46.72 37.35 REMARK 500 ASN A 178 58.89 38.06 REMARK 500 ASN A 199 62.29 35.35 REMARK 500 THR B 42 -50.05 -136.50 REMARK 500 LEU B 128 -65.94 -99.63 REMARK 500 ALA C 96 55.97 38.44 REMARK 500 ASN C 199 63.96 32.64 REMARK 500 ASN D 55 57.80 38.85 REMARK 500 ASP D 56 -5.16 71.13 REMARK 500 ASN D 159 15.30 59.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY B 112 ASN B 113 -57.41 REMARK 500 ASN B 113 PRO B 114 -149.26 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 GDP B 1200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP D 2200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FED RELATED DB: PDB REMARK 900 RELATED ID: 2EFE RELATED DB: PDB REMARK 900 RELATED ID: 2EFH RELATED DB: PDB DBREF 2EFC A 1 265 UNP Q9LT31 Q9LT31_ARATH 1 265 DBREF 2EFC C 1 265 UNP Q9LT31 Q9LT31_ARATH 1 265 DBREF 2EFC B 1 179 UNP Q9SN68 Q9SN68_ARATH 1 179 DBREF 2EFC D 1 179 UNP Q9SN68 Q9SN68_ARATH 1 179 SEQADV 2EFC GLY A -1 UNP Q9LT31 EXPRESSION TAG SEQADV 2EFC SER A 0 UNP Q9LT31 EXPRESSION TAG SEQADV 2EFC GLY C -1 UNP Q9LT31 EXPRESSION TAG SEQADV 2EFC SER C 0 UNP Q9LT31 EXPRESSION TAG SEQADV 2EFC GLY B -1 UNP Q9LT31 EXPRESSION TAG SEQADV 2EFC SER B 0 UNP Q9LT31 EXPRESSION TAG SEQADV 2EFC GLY D -1 UNP Q9LT31 EXPRESSION TAG SEQADV 2EFC SER D 0 UNP Q9LT31 EXPRESSION TAG SEQRES 1 A 267 GLY SER MET GLU ASN THR ASP VAL PHE LEU GLY LEU HIS SEQRES 2 A 267 ASP PHE LEU GLU ARG MET ARG LYS PRO SER ALA GLY ASP SEQRES 3 A 267 PHE VAL LYS SER ILE LYS SER PHE ILE VAL SER PHE SER SEQRES 4 A 267 ASN ASN ALA PRO ASP PRO GLU LYS ASP CYS ALA MET VAL SEQRES 5 A 267 GLN GLU PHE PHE SER LYS MET GLU ALA ALA PHE ARG ALA SEQRES 6 A 267 HIS PRO LEU TRP SER GLY CYS SER GLU GLU GLU LEU ASP SEQRES 7 A 267 SER ALA GLY ASP GLY LEU GLU LYS TYR VAL MET THR LYS SEQRES 8 A 267 LEU PHE THR ARG VAL PHE ALA SER ASN THR GLU GLU VAL SEQRES 9 A 267 ILE ALA ASP GLU LYS LEU PHE GLN LYS MET SER LEU VAL SEQRES 10 A 267 GLN GLN PHE ILE SER PRO GLU ASN LEU ASP ILE GLN PRO SEQRES 11 A 267 THR PHE GLN ASN GLU SER SER TRP LEU LEU ALA GLN LYS SEQRES 12 A 267 GLU LEU GLN LYS ILE ASN MET TYR LYS ALA PRO ARG ASP SEQRES 13 A 267 LYS LEU VAL CYS ILE LEU ASN CYS CYS LYS VAL ILE ASN SEQRES 14 A 267 ASN LEU LEU LEU ASN ALA SER ILE ALA SER ASN GLU ASN SEQRES 15 A 267 ALA PRO GLY ALA ASP GLU PHE LEU PRO VAL LEU ILE TYR SEQRES 16 A 267 VAL THR ILE LYS ALA ASN PRO PRO GLN LEU HIS SER ASN SEQRES 17 A 267 LEU LEU TYR ILE GLN ARG TYR ARG ARG GLU SER LYS LEU SEQRES 18 A 267 VAL GLY GLU ALA ALA TYR PHE PHE THR ASN ILE LEU SER SEQRES 19 A 267 ALA GLU SER PHE ILE SER ASN ILE ASP ALA LYS SER ILE SEQRES 20 A 267 SER LEU ASP GLU ALA GLU PHE GLU LYS ASN MET GLU SER SEQRES 21 A 267 ALA ARG ALA ARG ILE SER GLY SEQRES 1 B 181 GLY SER MET ALA ALA ALA GLY ASN LYS SER ILE ASN ALA SEQRES 2 B 181 LYS LEU VAL LEU LEU GLY ASP VAL GLY ALA GLY LYS SER SEQRES 3 B 181 SER LEU VAL LEU ARG PHE VAL LYS ASP GLN PHE VAL GLU SEQRES 4 B 181 PHE GLN GLU SER THR ILE GLY ALA ALA PHE PHE SER GLN SEQRES 5 B 181 THR LEU ALA VAL ASN ASP ALA THR VAL LYS PHE GLU ILE SEQRES 6 B 181 TRP ASP THR ALA GLY GLN GLU ARG TYR HIS SER LEU ALA SEQRES 7 B 181 PRO MET TYR TYR ARG GLY ALA ALA ALA ALA ILE ILE VAL SEQRES 8 B 181 PHE ASP VAL THR ASN GLN ALA SER PHE GLU ARG ALA LYS SEQRES 9 B 181 LYS TRP VAL GLN GLU LEU GLN ALA GLN GLY ASN PRO ASN SEQRES 10 B 181 MET VAL MET ALA LEU ALA GLY ASN LYS SER ASP LEU LEU SEQRES 11 B 181 ASP ALA ARG LYS VAL THR ALA GLU ASP ALA GLN THR TYR SEQRES 12 B 181 ALA GLN GLU ASN GLY LEU PHE PHE MET GLU THR SER ALA SEQRES 13 B 181 LYS THR ALA THR ASN VAL LYS GLU ILE PHE TYR GLU ILE SEQRES 14 B 181 ALA ARG ARG LEU PRO ARG VAL GLN PRO THR GLU ASN SEQRES 1 C 267 GLY SER MET GLU ASN THR ASP VAL PHE LEU GLY LEU HIS SEQRES 2 C 267 ASP PHE LEU GLU ARG MET ARG LYS PRO SER ALA GLY ASP SEQRES 3 C 267 PHE VAL LYS SER ILE LYS SER PHE ILE VAL SER PHE SER SEQRES 4 C 267 ASN ASN ALA PRO ASP PRO GLU LYS ASP CYS ALA MET VAL SEQRES 5 C 267 GLN GLU PHE PHE SER LYS MET GLU ALA ALA PHE ARG ALA SEQRES 6 C 267 HIS PRO LEU TRP SER GLY CYS SER GLU GLU GLU LEU ASP SEQRES 7 C 267 SER ALA GLY ASP GLY LEU GLU LYS TYR VAL MET THR LYS SEQRES 8 C 267 LEU PHE THR ARG VAL PHE ALA SER ASN THR GLU GLU VAL SEQRES 9 C 267 ILE ALA ASP GLU LYS LEU PHE GLN LYS MET SER LEU VAL SEQRES 10 C 267 GLN GLN PHE ILE SER PRO GLU ASN LEU ASP ILE GLN PRO SEQRES 11 C 267 THR PHE GLN ASN GLU SER SER TRP LEU LEU ALA GLN LYS SEQRES 12 C 267 GLU LEU GLN LYS ILE ASN MET TYR LYS ALA PRO ARG ASP SEQRES 13 C 267 LYS LEU VAL CYS ILE LEU ASN CYS CYS LYS VAL ILE ASN SEQRES 14 C 267 ASN LEU LEU LEU ASN ALA SER ILE ALA SER ASN GLU ASN SEQRES 15 C 267 ALA PRO GLY ALA ASP GLU PHE LEU PRO VAL LEU ILE TYR SEQRES 16 C 267 VAL THR ILE LYS ALA ASN PRO PRO GLN LEU HIS SER ASN SEQRES 17 C 267 LEU LEU TYR ILE GLN ARG TYR ARG ARG GLU SER LYS LEU SEQRES 18 C 267 VAL GLY GLU ALA ALA TYR PHE PHE THR ASN ILE LEU SER SEQRES 19 C 267 ALA GLU SER PHE ILE SER ASN ILE ASP ALA LYS SER ILE SEQRES 20 C 267 SER LEU ASP GLU ALA GLU PHE GLU LYS ASN MET GLU SER SEQRES 21 C 267 ALA ARG ALA ARG ILE SER GLY SEQRES 1 D 181 GLY SER MET ALA ALA ALA GLY ASN LYS SER ILE ASN ALA SEQRES 2 D 181 LYS LEU VAL LEU LEU GLY ASP VAL GLY ALA GLY LYS SER SEQRES 3 D 181 SER LEU VAL LEU ARG PHE VAL LYS ASP GLN PHE VAL GLU SEQRES 4 D 181 PHE GLN GLU SER THR ILE GLY ALA ALA PHE PHE SER GLN SEQRES 5 D 181 THR LEU ALA VAL ASN ASP ALA THR VAL LYS PHE GLU ILE SEQRES 6 D 181 TRP ASP THR ALA GLY GLN GLU ARG TYR HIS SER LEU ALA SEQRES 7 D 181 PRO MET TYR TYR ARG GLY ALA ALA ALA ALA ILE ILE VAL SEQRES 8 D 181 PHE ASP VAL THR ASN GLN ALA SER PHE GLU ARG ALA LYS SEQRES 9 D 181 LYS TRP VAL GLN GLU LEU GLN ALA GLN GLY ASN PRO ASN SEQRES 10 D 181 MET VAL MET ALA LEU ALA GLY ASN LYS SER ASP LEU LEU SEQRES 11 D 181 ASP ALA ARG LYS VAL THR ALA GLU ASP ALA GLN THR TYR SEQRES 12 D 181 ALA GLN GLU ASN GLY LEU PHE PHE MET GLU THR SER ALA SEQRES 13 D 181 LYS THR ALA THR ASN VAL LYS GLU ILE PHE TYR GLU ILE SEQRES 14 D 181 ALA ARG ARG LEU PRO ARG VAL GLN PRO THR GLU ASN HET GDP B1200 28 HET GDP D2200 28 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 5 GDP 2(C10 H15 N5 O11 P2) FORMUL 7 HOH *331(H2 O) HELIX 1 1 LYS A 19 SER A 21 5 3 HELIX 2 2 ALA A 22 PHE A 36 1 15 HELIX 3 3 ASP A 42 ALA A 63 1 22 HELIX 4 4 HIS A 64 SER A 68 5 5 HELIX 5 5 SER A 71 PHE A 95 1 25 HELIX 6 6 ASN A 98 GLN A 116 1 19 HELIX 7 7 SER A 120 ASP A 125 5 6 HELIX 8 8 GLN A 127 GLN A 131 5 5 HELIX 9 9 TRP A 136 LYS A 145 1 10 HELIX 10 10 ILE A 146 TYR A 149 5 4 HELIX 11 11 ALA A 151 SER A 177 1 27 HELIX 12 12 GLY A 183 ASN A 199 1 17 HELIX 13 13 GLN A 202 ARG A 214 1 13 HELIX 14 14 ARG A 215 LEU A 219 5 5 HELIX 15 15 VAL A 220 ASN A 239 1 20 HELIX 16 16 ASP A 248 ARG A 262 1 15 HELIX 17 17 GLY B 22 ASP B 33 1 12 HELIX 18 18 GLN B 69 LEU B 75 5 7 HELIX 19 19 ALA B 76 ARG B 81 1 6 HELIX 20 20 ASN B 94 GLY B 112 1 19 HELIX 21 21 THR B 134 ASN B 145 1 12 HELIX 22 22 ASN B 159 ARG B 170 1 12 HELIX 23 23 LYS C 19 SER C 21 5 3 HELIX 24 24 ALA C 22 ASN C 39 1 18 HELIX 25 25 ASP C 42 HIS C 64 1 23 HELIX 26 26 PRO C 65 SER C 68 5 4 HELIX 27 27 SER C 71 PHE C 95 1 25 HELIX 28 28 ASN C 98 GLN C 116 1 19 HELIX 29 29 SER C 120 ASP C 125 5 6 HELIX 30 30 GLN C 127 GLN C 131 5 5 HELIX 31 31 TRP C 136 LYS C 145 1 10 HELIX 32 32 ILE C 146 TYR C 149 5 4 HELIX 33 33 ALA C 151 SER C 177 1 27 HELIX 34 34 GLY C 183 ASN C 199 1 17 HELIX 35 35 GLN C 202 ARG C 214 1 13 HELIX 36 36 VAL C 220 ASN C 239 1 20 HELIX 37 37 ALA C 242 SER C 246 5 5 HELIX 38 38 ASP C 248 ARG C 262 1 15 HELIX 39 39 GLY D 22 ASP D 33 1 12 HELIX 40 40 GLN D 69 LEU D 75 5 7 HELIX 41 41 ALA D 76 ARG D 81 1 6 HELIX 42 42 ASN D 94 GLY D 112 1 19 HELIX 43 43 THR D 134 ASN D 145 1 12 HELIX 44 44 ASN D 159 ARG D 170 1 12 SHEET 1 A 6 PHE B 47 LEU B 52 0 SHEET 2 A 6 VAL B 59 ASP B 65 -1 O PHE B 61 N GLN B 50 SHEET 3 A 6 ILE B 9 LEU B 16 1 N LEU B 13 O GLU B 62 SHEET 4 A 6 ALA B 85 ASP B 91 1 O VAL B 89 N LEU B 16 SHEET 5 A 6 VAL B 117 ASN B 123 1 O ASN B 123 N PHE B 90 SHEET 6 A 6 PHE B 148 GLU B 151 1 O PHE B 148 N LEU B 120 SHEET 1 B 6 PHE D 47 LEU D 52 0 SHEET 2 B 6 VAL D 59 ASP D 65 -1 O ILE D 63 N PHE D 48 SHEET 3 B 6 ILE D 9 LEU D 16 1 N ILE D 9 O LYS D 60 SHEET 4 B 6 ALA D 85 ASP D 91 1 O VAL D 89 N LEU D 16 SHEET 5 B 6 VAL D 117 ASN D 123 1 O ASN D 123 N PHE D 90 SHEET 6 B 6 PHE D 148 GLU D 151 1 O PHE D 148 N LEU D 120 CISPEP 1 SER A 68 GLY A 69 0 15.48 CISPEP 2 SER C 68 GLY C 69 0 20.97 SITE 1 AC1 19 ASN A 180 ASP A 185 HOH A 323 ASP B 18 SITE 2 AC1 19 GLY B 20 ALA B 21 GLY B 22 LYS B 23 SITE 3 AC1 19 SER B 24 SER B 25 ASN B 123 LYS B 124 SITE 4 AC1 19 ASP B 126 SER B 153 ALA B 154 LYS B 155 SITE 5 AC1 19 HOH B1204 HOH B1208 HOH B1232 SITE 1 AC2 19 ASN C 180 ASP C 185 HOH C 280 ASP D 18 SITE 2 AC2 19 GLY D 20 ALA D 21 GLY D 22 LYS D 23 SITE 3 AC2 19 SER D 24 SER D 25 ASN D 123 LYS D 124 SITE 4 AC2 19 ASP D 126 LEU D 127 SER D 153 ALA D 154 SITE 5 AC2 19 LYS D 155 HOH D2208 HOH D2246 CRYST1 58.377 58.474 68.714 81.68 86.89 72.97 P 1 2 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 0.017130 -0.005246 -0.000227 0.00000 SCALE2 0.000000 0.017886 -0.002435 0.00000 SCALE3 0.000000 0.000000 0.014709 0.00000