HEADER TRANSPORT PROTEIN 09-JUL-12 4G01 TITLE ARA7-GDP-CA2+/VPS9A COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 9A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: VPS9 DOMAIN, UNP RESIDUES 1-265; COMPND 5 SYNONYM: VPS9A, ATVSP9A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RAS-RELATED PROTEIN RABF2B; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: SMALL GTPASE, UNP RESIDUES 1-179; COMPND 11 SYNONYM: ARA7, ATRABF2B, RAS-RELATED PROTEIN ARA-7, RAS-RELATED COMPND 12 PROTEIN RAB5B, ATRAB5B; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: VPS9A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 10 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 11 ORGANISM_TAXID: 3702; SOURCE 12 GENE: ARA-7; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GTPASE-GDP-METAL-GEF COMPLEX, VPS9 DOMAIN, RAS SUPER FAMILY, GUANINE KEYWDS 2 NUCLEOTIDE EXCHANGE FACTOR, SMALL GTPASE, GDP/GTP BINDING, DIVALENT KEYWDS 3 METAL BINDING, GERANYLGERANYLATION, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.IHARA REVDAT 3 08-NOV-23 4G01 1 REMARK SEQADV LINK REVDAT 2 07-AUG-13 4G01 1 JRNL REVDAT 1 27-FEB-13 4G01 0 JRNL AUTH T.UEJIMA,K.IHARA,M.SUNADA,M.KAWASAKI,T.UEDA,R.KATO,A.NAKANO, JRNL AUTH 2 S.WAKATSUKI JRNL TITL DIRECT METAL RECOGNITION BY GUANINE NUCLEOTIDE-EXCHANGE JRNL TITL 2 FACTOR IN THE INITIAL STEP OF THE EXCHANGE REACTION JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 345 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 23519409 JRNL DOI 10.1107/S0907444912047294 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 21156 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1140 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1528 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3171 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 261 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.82000 REMARK 3 B22 (A**2) : 1.50000 REMARK 3 B33 (A**2) : -0.69000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.305 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.247 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.167 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.454 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.882 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3260 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4411 ; 1.374 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 400 ; 5.882 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;38.521 ;25.226 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 572 ;17.061 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;19.439 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 492 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2451 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2007 ; 0.781 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3225 ; 1.507 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1253 ; 2.283 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1186 ; 3.844 ; 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4G01 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073566. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22345 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 55.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.13000 REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.69100 REMARK 200 FOR SHELL : 2.800 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: PDB ENTRY 2EFC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 200MM CALCIUM ACETATE, PH REMARK 280 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 34.17450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.89350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.06950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.89350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.17450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.06950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 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 MET A 17 REMARK 465 ARG A 18 REMARK 465 LYS A 19 REMARK 465 PRO A 20 REMARK 465 SER A 21 REMARK 465 ALA A 22 REMARK 465 GLY A 23 REMARK 465 ASP A 24 REMARK 465 PHE A 25 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 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 O3' GDP B 200 O HOH B 375 2.17 REMARK 500 OD1 ASN B 113 O HOH B 340 2.19 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 214 NE - CZ - NH1 ANGL. DEV. = 3.7 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 ASN A 199 59.65 34.41 REMARK 500 ALA B 157 0.72 89.42 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 CA A 300 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 182 O REMARK 620 2 ASP A 185 OD2 88.1 REMARK 620 3 HOH A 404 O 78.2 135.5 REMARK 620 4 HOH A 410 O 100.7 66.1 157.8 REMARK 620 5 HOH A 485 O 91.2 61.8 76.3 125.9 REMARK 620 6 SER B 24 OG 81.8 139.4 80.5 77.4 156.7 REMARK 620 7 GDP B 200 O2B 164.6 105.8 87.2 91.1 89.8 91.4 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP B 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EFC RELATED DB: PDB REMARK 900 ARA7-GDP/VPS9A REMARK 900 RELATED ID: 2EFD RELATED DB: PDB REMARK 900 ARA7/VPS9A REMARK 900 RELATED ID: 2EFE RELATED DB: PDB REMARK 900 ARA7-GDPNH2/VPS9A REMARK 900 RELATED ID: 2EFH RELATED DB: PDB REMARK 900 ARA7-GDP/VPS9A(D185N) DBREF 4G01 A 1 265 UNP Q9LT31 VPS9A_ARATH 1 265 DBREF 4G01 B 1 179 UNP Q9SN68 RAF2B_ARATH 1 179 SEQADV 4G01 GLY A -1 UNP Q9LT31 EXPRESSION TAG SEQADV 4G01 SER A 0 UNP Q9LT31 EXPRESSION TAG SEQADV 4G01 GLY B -1 UNP Q9SN68 EXPRESSION TAG SEQADV 4G01 SER B 0 UNP Q9SN68 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 HET CA A 300 1 HET GDP B 200 28 HETNAM CA CALCIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 3 CA CA 2+ FORMUL 4 GDP C10 H15 N5 O11 P2 FORMUL 5 HOH *261(H2 O) HELIX 1 1 VAL A 26 SER A 37 1 12 HELIX 2 2 ASP A 42 HIS A 64 1 23 HELIX 3 3 PRO A 65 SER A 68 5 4 HELIX 4 4 SER A 71 PHE A 95 1 25 HELIX 5 5 ASN A 98 GLN A 116 1 19 HELIX 6 6 PRO A 121 ASP A 125 5 5 HELIX 7 7 THR A 129 GLN A 144 1 16 HELIX 8 8 LYS A 145 TYR A 149 5 5 HELIX 9 9 ALA A 151 SER A 177 1 27 HELIX 10 10 GLY A 183 ASN A 199 1 17 HELIX 11 11 GLN A 202 ARG A 214 1 13 HELIX 12 12 ARG A 215 LEU A 219 5 5 HELIX 13 13 VAL A 220 ASN A 239 1 20 HELIX 14 14 ALA A 242 SER A 246 5 5 HELIX 15 15 ASP A 248 ALA A 261 1 14 HELIX 16 16 GLY B 22 PHE B 35 1 14 HELIX 17 17 VAL B 36 PHE B 38 5 3 HELIX 18 18 GLN B 69 SER B 74 5 6 HELIX 19 19 LEU B 75 ARG B 81 1 7 HELIX 20 20 ASN B 94 GLY B 112 1 19 HELIX 21 21 LEU B 127 ARG B 131 5 5 HELIX 22 22 THR B 134 ASN B 145 1 12 HELIX 23 23 ASN B 159 LEU B 171 1 13 SHEET 1 A 7 SER B 41 ILE B 43 0 SHEET 2 A 7 PHE B 47 VAL B 54 -1 O SER B 49 N THR B 42 SHEET 3 A 7 ALA B 57 TRP B 64 -1 O VAL B 59 N LEU B 52 SHEET 4 A 7 ILE B 9 LEU B 16 1 N ILE B 9 O LYS B 60 SHEET 5 A 7 ALA B 85 ASP B 91 1 O VAL B 89 N LEU B 16 SHEET 6 A 7 VAL B 117 ASN B 123 1 O ALA B 119 N ILE B 88 SHEET 7 A 7 PHE B 148 GLU B 151 1 O PHE B 148 N LEU B 120 LINK O PRO A 182 CA CA A 300 1555 1555 2.35 LINK OD2 ASP A 185 CA CA A 300 1555 1555 2.48 LINK CA CA A 300 O HOH A 404 1555 1555 2.43 LINK CA CA A 300 O HOH A 410 1555 1555 2.40 LINK CA CA A 300 O HOH A 485 1555 1555 2.54 LINK CA CA A 300 OG SER B 24 1555 1555 2.38 LINK CA CA A 300 O2B GDP B 200 1555 1555 2.24 CISPEP 1 ASN B 55 ASP B 56 0 -19.57 SITE 1 AC1 7 PRO A 182 ASP A 185 HOH A 404 HOH A 410 SITE 2 AC1 7 HOH A 485 SER B 24 GDP B 200 SITE 1 AC2 19 ASN A 180 CA A 300 HOH A 404 HOH A 485 SITE 2 AC2 19 GLY B 20 ALA B 21 GLY B 22 LYS B 23 SITE 3 AC2 19 SER B 24 SER B 25 ASN B 123 LYS B 124 SITE 4 AC2 19 ASP B 126 LEU B 127 SER B 153 ALA B 154 SITE 5 AC2 19 LYS B 155 HOH B 322 HOH B 375 CRYST1 68.349 76.139 81.787 90.00 90.00 90.00 P 21 21 21 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 0.014631 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013134 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012227 0.00000