PDB Short entry for 1S9D HEADER PROTEIN TRANSPORT/EXCHANGE FACTOR 04-FEB-04 1S9D TITLE ARF1[DELTA 1-17]-GDP-MG IN COMPLEX WITH BREFELDIN A AND A SEC7 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYLATION FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 18-181; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ARNO; COMPND 8 CHAIN: E; COMPND 9 FRAGMENT: SEC7 DOMAIN (RESIDUES 50-252); COMPND 10 SYNONYM: ARF NUCLEOTIDE-BINDING SITE OPENER, CYTOHESIN 2, ARF COMPND 11 EXCHANGE FACTOR; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 GENE: ARF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 GOLD; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: PSCD2, ARNO; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21 GOLD; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET11D KEYWDS PROTEIN TRANSPORT/EXCHANGE FACTOR, PROTEIN TRANSPORT-EXCHANGE FACTOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.RENAULT,B.GUIBERT,J.CHERFILS REVDAT 6 23-AUG-23 1S9D 1 REMARK REVDAT 5 27-OCT-21 1S9D 1 REMARK SEQADV LINK REVDAT 4 11-OCT-17 1S9D 1 REMARK REVDAT 3 13-JUL-11 1S9D 1 VERSN REVDAT 2 24-FEB-09 1S9D 1 VERSN REVDAT 1 10-FEB-04 1S9D 0 SPRSDE 10-FEB-04 1S9D 1R8R JRNL AUTH L.RENAULT,B.GUIBERT,J.CHERFILS JRNL TITL STRUCTURAL SNAPSHOTS OF THE MECHANISM AND INHIBITION OF A JRNL TITL 2 GUANINE NUCLEOTIDE EXCHANGE FACTOR JRNL REF NATURE V. 426 525 2003 JRNL REFN ISSN 0028-0836 JRNL PMID 14654833 JRNL DOI 10.1038/NATURE02197 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 41588 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2225 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 19 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3171 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 181 REMARK 3 BIN FREE R VALUE : 0.2450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2830 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 286 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 22.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.95000 REMARK 3 B22 (A**2) : -1.95000 REMARK 3 B33 (A**2) : 3.89000 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): 0.111 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.112 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.786 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2942 ; 0.025 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2646 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3974 ; 1.940 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6146 ; 0.999 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 345 ; 5.862 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 435 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3218 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 598 ; 0.006 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 638 ; 0.226 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3246 ; 0.256 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1682 ; 0.090 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 231 ; 0.176 ; 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): 15 ; 0.249 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 57 ; 0.284 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.148 ; 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): 1728 ; 1.233 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2781 ; 2.081 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1214 ; 3.243 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1193 ; 5.065 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 18 A 178 REMARK 3 RESIDUE RANGE : A 401 A 402 REMARK 3 ORIGIN FOR THE GROUP (A): 39.7581 16.4036 32.9009 REMARK 3 T TENSOR REMARK 3 T11: 0.1086 T22: 0.0892 REMARK 3 T33: 0.1244 T12: 0.0016 REMARK 3 T13: -0.0001 T23: 0.0196 REMARK 3 L TENSOR REMARK 3 L11: 2.4826 L22: 1.1361 REMARK 3 L33: 1.0024 L12: 0.2967 REMARK 3 L13: 0.0892 L23: -0.3112 REMARK 3 S TENSOR REMARK 3 S11: -0.1139 S12: 0.0873 S13: 0.1898 REMARK 3 S21: 0.0578 S22: -0.0812 S23: -0.1553 REMARK 3 S31: -0.0553 S32: 0.0467 S33: 0.1951 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 57 E 249 REMARK 3 ORIGIN FOR THE GROUP (A): 22.9252 -5.5566 23.5297 REMARK 3 T TENSOR REMARK 3 T11: 0.1718 T22: 0.1708 REMARK 3 T33: 0.0873 T12: -0.0172 REMARK 3 T13: 0.0124 T23: -0.0745 REMARK 3 L TENSOR REMARK 3 L11: 0.9489 L22: 2.2842 REMARK 3 L33: 1.1349 L12: -0.3036 REMARK 3 L13: 0.1546 L23: 0.4855 REMARK 3 S TENSOR REMARK 3 S11: 0.0774 S12: 0.1902 S13: -0.1816 REMARK 3 S21: -0.1310 S22: 0.0320 S23: -0.0772 REMARK 3 S31: 0.2113 S32: 0.0849 S33: -0.1094 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 1S9D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1000021531. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980 REMARK 200 MONOCHROMATOR : DOUBLE SI CRYSTALS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43814 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 12.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.2000 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) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 12.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.40500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 (MOLREP) REMARK 200 STARTING MODEL: PDB ENTRY 1RRG AND COORDINATES OF ARF1[D1-17]/GEA2 REMARK 200 -SEC7 (GOLDBERG, J., (1998) CELL 95(2): 237-48) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 29% PEG 3350, 40MM NH4CL, 40MM REMARK 280 POTASSIUM FORMATE, 100MM TRIS, PH 8, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 37.26700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 55.73100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.73100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.63350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.73100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 55.73100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.90050 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.73100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.73100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 18.63350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 55.73100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.73100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.90050 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 37.26700 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 UNIT CONSISTS OF A QUATERNARY COMPLEX WITH 2 REMARK 300 PROTEINS (CHAIN A AND E) AND IS IDENTICAL TO THE ASYMMETRIC UNIT. 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: 4250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E 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 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 E 395 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 LEU A 39 REMARK 465 GLY A 40 REMARK 465 GLU A 41 REMARK 465 ILE A 42 REMARK 465 VAL A 43 REMARK 465 THR A 44 REMARK 465 ASN A 179 REMARK 465 GLN A 180 REMARK 465 LYS A 181 REMARK 465 LEU E 50 REMARK 465 GLU E 51 REMARK 465 ALA E 52 REMARK 465 ASN E 53 REMARK 465 GLU E 54 REMARK 465 GLY E 55 REMARK 465 SER E 56 REMARK 465 GLY E 250 REMARK 465 ASN E 251 REMARK 465 ASP E 252 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 NZ LYS A 38 O HOH A 404 1.93 REMARK 500 OD1 ASN A 101 O HOH A 435 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 22 SD MET A 22 CE -0.445 REMARK 500 GLU A 106 CD GLU A 106 OE1 0.085 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 ASP A 129 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG E 69 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG E 152 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG E 162 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG E 162 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP E 206 CB - CG - OD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 31 OG1 REMARK 620 2 GDP A 401 O1B 90.7 REMARK 620 3 HOH A 419 O 173.9 95.4 REMARK 620 4 HOH A 432 O 88.2 98.4 90.4 REMARK 620 5 HOH A 458 O 90.0 89.3 90.6 172.0 REMARK 620 6 HOH A 544 O 86.3 172.8 87.7 88.0 84.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AFB A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1R8M RELATED DB: PDB REMARK 900 SEC7 DOMAIN OF THE ARF EXCHANGE FACTOR ARNO WITH BREFELDIN A- REMARK 900 SENSITIZING MUTATIONS REMARK 900 RELATED ID: 1PBV RELATED DB: PDB REMARK 900 WILD TYPE SEC7 DOMAIN OF THE EXCHANGE FACTOR ARNO REMARK 900 RELATED ID: 1R8Q RELATED DB: PDB REMARK 900 FULL-LENGTH ARF1-GDP-MG IN COMPLEX WITH BREFELDIN A AND A SEC7 REMARK 900 DOMAIN REMARK 900 RELATED ID: 1R8S RELATED DB: PDB REMARK 900 ARF1[D1-17]-GDP IN COMPLEX WITH A SEC7 DOMAIN CARRYING THE MUTATION REMARK 900 OF THE CATALYTIC GLUTAMATE TO LYSINE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE ENGINEERED MUTATIONS IN THE ARNO STRUCTURE REMARK 999 (F190Y, A191S, S198D, P208M) ARE BREFELDIN A- REMARK 999 SENSITIZING MUTATIONS. DBREF 1S9D A 18 181 UNP P84080 ARF1_BOVIN 17 180 DBREF 1S9D E 50 252 UNP Q99418 CYH2_HUMAN 50 252 SEQADV 1S9D CME E 174 UNP Q99418 CYS 174 MODIFIED RESIDUE SEQADV 1S9D TYR E 190 UNP Q99418 PHE 190 ENGINEERED MUTATION SEQADV 1S9D SER E 191 UNP Q99418 ALA 191 ENGINEERED MUTATION SEQADV 1S9D ASP E 198 UNP Q99418 SER 198 ENGINEERED MUTATION SEQADV 1S9D MET E 208 UNP Q99418 PRO 208 ENGINEERED MUTATION SEQRES 1 A 164 MET ARG ILE LEU MET VAL GLY LEU ASP ALA ALA GLY LYS SEQRES 2 A 164 THR THR ILE LEU TYR LYS LEU LYS LEU GLY GLU ILE VAL SEQRES 3 A 164 THR THR ILE PRO THR ILE GLY PHE ASN VAL GLU THR VAL SEQRES 4 A 164 GLU TYR LYS ASN ILE SER PHE THR VAL TRP ASP VAL GLY SEQRES 5 A 164 GLY GLN ASP LYS ILE ARG PRO LEU TRP ARG HIS TYR PHE SEQRES 6 A 164 GLN ASN THR GLN GLY LEU ILE PHE VAL VAL ASP SER ASN SEQRES 7 A 164 ASP ARG GLU ARG VAL ASN GLU ALA ARG GLU GLU LEU MET SEQRES 8 A 164 ARG MET LEU ALA GLU ASP GLU LEU ARG ASP ALA VAL LEU SEQRES 9 A 164 LEU VAL PHE ALA ASN LYS GLN ASP LEU PRO ASN ALA MET SEQRES 10 A 164 ASN ALA ALA GLU ILE THR ASP LYS LEU GLY LEU HIS SER SEQRES 11 A 164 LEU ARG HIS ARG ASN TRP TYR ILE GLN ALA THR CYS ALA SEQRES 12 A 164 THR SER GLY ASP GLY LEU TYR GLU GLY LEU ASP TRP LEU SEQRES 13 A 164 SER ASN GLN LEU ARG ASN GLN LYS SEQRES 1 E 203 LEU GLU ALA ASN GLU GLY SER LYS THR LEU GLN ARG ASN SEQRES 2 E 203 ARG LYS MET ALA MET GLY ARG LYS LYS PHE ASN MET ASP SEQRES 3 E 203 PRO LYS LYS GLY ILE GLN PHE LEU VAL GLU ASN GLU LEU SEQRES 4 E 203 LEU GLN ASN THR PRO GLU GLU ILE ALA ARG PHE LEU TYR SEQRES 5 E 203 LYS GLY GLU GLY LEU ASN LYS THR ALA ILE GLY ASP TYR SEQRES 6 E 203 LEU GLY GLU ARG GLU GLU LEU ASN LEU ALA VAL LEU HIS SEQRES 7 E 203 ALA PHE VAL ASP LEU HIS GLU PHE THR ASP LEU ASN LEU SEQRES 8 E 203 VAL GLN ALA LEU ARG GLN PHE LEU TRP SER PHE ARG LEU SEQRES 9 E 203 PRO GLY GLU ALA GLN LYS ILE ASP ARG MET MET GLU ALA SEQRES 10 E 203 PHE ALA GLN ARG TYR CYS LEU CME ASN PRO GLY VAL PHE SEQRES 11 E 203 GLN SER THR ASP THR CYS TYR VAL LEU SER TYR SER VAL SEQRES 12 E 203 ILE MET LEU ASN THR ASP LEU HIS ASN PRO ASN VAL ARG SEQRES 13 E 203 ASP LYS MET GLY LEU GLU ARG PHE VAL ALA MET ASN ARG SEQRES 14 E 203 GLY ILE ASN GLU GLY GLY ASP LEU PRO GLU GLU LEU LEU SEQRES 15 E 203 ARG ASN LEU TYR ASP SER ILE ARG ASN GLU PRO PHE LYS SEQRES 16 E 203 ILE PRO GLU ASP ASP GLY ASN ASP MODRES 1S9D CME E 174 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE HET CME E 174 10 HET MG A 402 1 HET GDP A 401 28 HET AFB A 403 20 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM AFB 1,6,7,8,9,11A,12,13,14,14A-DECAHYDRO-1,13-DIHYDROXY-6- HETNAM 2 AFB METHYL-4H-CYCLOPENT[F]OXACYCLOTRIDECIN-4-ONE HETSYN AFB BREFELDIN A FORMUL 2 CME C5 H11 N O3 S2 FORMUL 3 MG MG 2+ FORMUL 4 GDP C10 H15 N5 O11 P2 FORMUL 5 AFB C16 H24 O4 FORMUL 6 HOH *286(H2 O) HELIX 1 1 GLY A 29 LYS A 38 1 10 HELIX 2 2 GLN A 71 GLN A 83 5 13 HELIX 3 3 ASP A 96 GLU A 98 5 3 HELIX 4 4 ARG A 99 ALA A 112 1 14 HELIX 5 5 GLU A 113 ARG A 117 5 5 HELIX 6 6 ASN A 135 LEU A 143 1 9 HELIX 7 7 GLY A 144 LEU A 148 5 5 HELIX 8 8 GLY A 165 ARG A 178 1 14 HELIX 9 9 LYS E 57 ASP E 75 1 19 HELIX 10 10 ASP E 75 ASN E 86 1 12 HELIX 11 11 THR E 92 TYR E 101 1 10 HELIX 12 12 ASN E 107 GLY E 116 1 10 HELIX 13 13 GLU E 119 ASP E 131 1 13 HELIX 14 14 ASN E 139 LEU E 148 1 10 HELIX 15 15 GLU E 156 ASN E 175 1 20 HELIX 16 16 SER E 181 ASN E 201 1 21 HELIX 17 17 GLY E 209 ASN E 217 1 9 HELIX 18 18 PRO E 227 GLU E 241 1 15 SHEET 1 A 6 THR A 55 TYR A 58 0 SHEET 2 A 6 ILE A 61 VAL A 65 -1 O PHE A 63 N VAL A 56 SHEET 3 A 6 ILE A 20 VAL A 23 1 N MET A 22 O THR A 64 SHEET 4 A 6 GLY A 87 ASP A 93 1 O ILE A 89 N LEU A 21 SHEET 5 A 6 VAL A 120 ASN A 126 1 O VAL A 120 N LEU A 88 SHEET 6 A 6 TRP A 153 ALA A 157 1 O TYR A 154 N VAL A 123 LINK C LEU E 173 N CME E 174 1555 1555 1.35 LINK C CME E 174 N ASN E 175 1555 1555 1.33 LINK OG1 THR A 31 MG MG A 402 1555 1555 2.05 LINK O1B GDP A 401 MG MG A 402 1555 1555 2.08 LINK MG MG A 402 O HOH A 419 1555 1555 2.05 LINK MG MG A 402 O HOH A 432 1555 1555 2.03 LINK MG MG A 402 O HOH A 458 1555 1555 2.20 LINK MG MG A 402 O HOH A 544 1555 1555 2.13 SITE 1 AC1 6 THR A 31 GDP A 401 HOH A 419 HOH A 432 SITE 2 AC1 6 HOH A 458 HOH A 544 SITE 1 AC2 23 ALA A 27 ALA A 28 GLY A 29 LYS A 30 SITE 2 AC2 23 THR A 31 THR A 32 ASN A 126 LYS A 127 SITE 3 AC2 23 ASP A 129 LEU A 130 CYS A 159 ALA A 160 SITE 4 AC2 23 THR A 161 MG A 402 HOH A 419 HOH A 452 SITE 5 AC2 23 HOH A 458 HOH A 464 HOH A 482 HOH A 490 SITE 6 AC2 23 HOH A 500 HOH A 512 HOH A 543 SITE 1 AC3 11 VAL A 53 THR A 64 TRP A 66 ASP A 67 SITE 2 AC3 11 TRP A 78 TYR A 81 HOH A 438 HOH A 446 SITE 3 AC3 11 HOH A 469 TYR E 190 MET E 194 CRYST1 111.462 111.462 74.534 90.00 90.00 90.00 P 41 21 2 8 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 0.008972 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008972 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013417 0.00000