PDB Short entry for 1Z0D HEADER PROTEIN TRANSPORT 01-MAR-05 1Z0D TITLE GDP-BOUND RAB5C GTPASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-5C; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: GTPASE DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: RAB5C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) CODON PLUS-RIL CELLS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: GST FUSION, PGEX; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T1 KEYWDS RAB GTPASE, RAB5C, VESICULAR TRAFFICKING, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.EATHIRAJ,X.PAN,C.RITACCO,D.G.LAMBRIGHT REVDAT 5 03-APR-24 1Z0D 1 REMARK REVDAT 4 14-FEB-24 1Z0D 1 REMARK REVDAT 3 20-OCT-21 1Z0D 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1Z0D 1 VERSN REVDAT 1 26-JUL-05 1Z0D 0 JRNL AUTH S.EATHIRAJ,X.PAN,C.RITACCO,D.G.LAMBRIGHT JRNL TITL STRUCTURAL BASIS OF FAMILY-WIDE RAB GTPASE RECOGNITION BY JRNL TITL 2 RABENOSYN-5. JRNL REF NATURE V. 436 415 2005 JRNL REFN ISSN 0028-0836 JRNL PMID 16034420 JRNL DOI 10.1038/NATURE03798 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 18123 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 983 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) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1272 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 65 REMARK 3 BIN FREE R VALUE : 0.3680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2504 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 409 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.66000 REMARK 3 B22 (A**2) : 1.28000 REMARK 3 B33 (A**2) : -0.62000 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): 0.290 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.225 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.144 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.505 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2613 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3560 ; 1.112 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 328 ; 5.370 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 105 ;35.358 ;24.762 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 415 ;12.870 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;12.077 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 416 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1919 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1349 ; 0.189 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1809 ; 0.297 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 415 ; 0.132 ; 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): 69 ; 0.176 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 41 ; 0.111 ; 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): 1672 ; 0.459 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2607 ; 0.825 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1088 ; 1.046 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 953 ; 1.758 ; 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 1Z0D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032138. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-AUG-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19641 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.0000 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) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.40700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 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: POLYALANINE RAB3A GTPASE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 4000, 200MM LITHIUM SULFATE, REMARK 280 50MM NA ACETATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 19.20050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.80500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.46550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.80500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.20050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.46550 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 17 REMARK 465 SER A 18 REMARK 465 GLY C 17 REMARK 465 SER C 18 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 ILE A 19 CG1 CG2 CD1 REMARK 470 ASP A 66 CG OD1 OD2 REMARK 470 ASP A 67 CG OD1 OD2 REMARK 470 LYS A 181 CG CD CE NZ REMARK 470 ILE C 19 CG1 CG2 CD1 REMARK 470 GLU C 48 CG CD OE1 OE2 REMARK 470 TYR C 49 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN C 50 CG CD OE1 NE2 REMARK 470 GLU C 51 CG CD OE1 OE2 REMARK 470 SER C 52 OG REMARK 470 ASP C 66 CG OD1 OD2 REMARK 470 ASP C 67 CG OD1 OD2 REMARK 470 LYS C 71 CG CD CE NZ REMARK 470 ARG C 82 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 111 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 117 CG CD CE NZ REMARK 470 ARG C 121 CG CD NE CZ NH1 NH2 REMARK 470 GLN C 122 CG CD OE1 NE2 REMARK 470 GLN C 147 CG CD OE1 NE2 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 O HOH A 753 O HOH A 757 2.19 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 ASP A 66 -122.83 51.85 REMARK 500 ASP C 66 75.62 32.35 REMARK 500 ASP C 67 -19.44 80.61 REMARK 500 ALA C 168 -0.06 76.35 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 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 35 OG REMARK 620 2 GDP A 700 O2B 86.0 REMARK 620 3 HOH A 706 O 170.0 88.9 REMARK 620 4 HOH A 709 O 79.8 90.7 91.7 REMARK 620 5 HOH A 718 O 92.4 91.9 96.4 171.6 REMARK 620 6 HOH A 724 O 85.8 171.3 98.8 85.0 91.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 800 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER C 35 OG REMARK 620 2 GDP C 900 O2B 87.5 REMARK 620 3 HOH C 907 O 85.1 83.2 REMARK 620 4 HOH C 913 O 84.6 165.4 83.9 REMARK 620 5 HOH C 916 O 175.4 93.1 90.5 93.9 REMARK 620 6 HOH C 923 O 83.1 97.1 168.2 94.1 101.3 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 PO4 A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP C 900 DBREF 1Z0D A 19 183 UNP P35278 RAB5C_MOUSE 19 183 DBREF 1Z0D C 19 183 UNP P35278 RAB5C_MOUSE 19 183 SEQADV 1Z0D GLY A 17 UNP P35278 CLONING ARTIFACT SEQADV 1Z0D SER A 18 UNP P35278 CLONING ARTIFACT SEQADV 1Z0D LEU A 80 UNP P35278 GLN 80 ENGINEERED MUTATION SEQADV 1Z0D GLY C 17 UNP P35278 CLONING ARTIFACT SEQADV 1Z0D SER C 18 UNP P35278 CLONING ARTIFACT SEQADV 1Z0D LEU C 80 UNP P35278 GLN 80 ENGINEERED MUTATION SEQRES 1 A 167 GLY SER ILE CYS GLN PHE LYS LEU VAL LEU LEU GLY GLU SEQRES 2 A 167 SER ALA VAL GLY LYS SER SER LEU VAL LEU ARG PHE VAL SEQRES 3 A 167 LYS GLY GLN PHE HIS GLU TYR GLN GLU SER THR ILE GLY SEQRES 4 A 167 ALA ALA PHE LEU THR GLN THR VAL CYS LEU ASP ASP THR SEQRES 5 A 167 THR VAL LYS PHE GLU ILE TRP ASP THR ALA GLY LEU GLU SEQRES 6 A 167 ARG TYR HIS SER LEU ALA PRO MET TYR TYR ARG GLY ALA SEQRES 7 A 167 GLN ALA ALA ILE VAL VAL TYR ASP ILE THR ASN THR ASP SEQRES 8 A 167 THR PHE ALA ARG ALA LYS ASN TRP VAL LYS GLU LEU GLN SEQRES 9 A 167 ARG GLN ALA SER PRO ASN ILE VAL ILE ALA LEU ALA GLY SEQRES 10 A 167 ASN LYS ALA ASP LEU ALA SER LYS ARG ALA VAL GLU PHE SEQRES 11 A 167 GLN GLU ALA GLN ALA TYR ALA ASP ASP ASN SER LEU LEU SEQRES 12 A 167 PHE MET GLU THR SER ALA LYS THR ALA MET ASN VAL ASN SEQRES 13 A 167 GLU ILE PHE MET ALA ILE ALA LYS LYS LEU PRO SEQRES 1 C 167 GLY SER ILE CYS GLN PHE LYS LEU VAL LEU LEU GLY GLU SEQRES 2 C 167 SER ALA VAL GLY LYS SER SER LEU VAL LEU ARG PHE VAL SEQRES 3 C 167 LYS GLY GLN PHE HIS GLU TYR GLN GLU SER THR ILE GLY SEQRES 4 C 167 ALA ALA PHE LEU THR GLN THR VAL CYS LEU ASP ASP THR SEQRES 5 C 167 THR VAL LYS PHE GLU ILE TRP ASP THR ALA GLY LEU GLU SEQRES 6 C 167 ARG TYR HIS SER LEU ALA PRO MET TYR TYR ARG GLY ALA SEQRES 7 C 167 GLN ALA ALA ILE VAL VAL TYR ASP ILE THR ASN THR ASP SEQRES 8 C 167 THR PHE ALA ARG ALA LYS ASN TRP VAL LYS GLU LEU GLN SEQRES 9 C 167 ARG GLN ALA SER PRO ASN ILE VAL ILE ALA LEU ALA GLY SEQRES 10 C 167 ASN LYS ALA ASP LEU ALA SER LYS ARG ALA VAL GLU PHE SEQRES 11 C 167 GLN GLU ALA GLN ALA TYR ALA ASP ASP ASN SER LEU LEU SEQRES 12 C 167 PHE MET GLU THR SER ALA LYS THR ALA MET ASN VAL ASN SEQRES 13 C 167 GLU ILE PHE MET ALA ILE ALA LYS LYS LEU PRO HET PO4 A 600 5 HET MG A 601 1 HET GDP A 700 28 HET MG C 800 1 HET GDP C 900 28 HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 3 PO4 O4 P 3- FORMUL 4 MG 2(MG 2+) FORMUL 5 GDP 2(C10 H15 N5 O11 P2) FORMUL 8 HOH *409(H2 O) HELIX 1 1 GLY A 33 GLY A 44 1 12 HELIX 2 2 TYR A 83 LEU A 86 5 4 HELIX 3 3 ALA A 87 ARG A 92 1 6 HELIX 4 4 ASN A 105 ALA A 123 1 19 HELIX 5 5 LYS A 135 ARG A 142 5 8 HELIX 6 6 GLU A 145 ASN A 156 1 12 HELIX 7 7 ASN A 170 LEU A 182 1 13 HELIX 8 8 GLY C 33 GLY C 44 1 12 HELIX 9 9 GLY C 79 SER C 85 5 7 HELIX 10 10 LEU C 86 ARG C 92 1 7 HELIX 11 11 ASN C 105 ALA C 123 1 19 HELIX 12 12 LYS C 135 ARG C 142 5 8 HELIX 13 13 GLU C 145 ASN C 156 1 12 HELIX 14 14 ASN C 170 LEU C 182 1 13 SHEET 1 A 6 GLY A 55 LEU A 65 0 SHEET 2 A 6 THR A 68 ALA A 78 -1 O ILE A 74 N LEU A 59 SHEET 3 A 6 CYS A 20 LEU A 27 1 N CYS A 20 O THR A 69 SHEET 4 A 6 ALA A 96 ASP A 102 1 O VAL A 100 N LEU A 27 SHEET 5 A 6 VAL A 128 ASN A 134 1 O ALA A 130 N ALA A 97 SHEET 6 A 6 LEU A 159 GLU A 162 1 O LEU A 159 N LEU A 131 SHEET 1 B 6 ALA C 56 LEU C 65 0 SHEET 2 B 6 THR C 68 THR C 77 -1 O ILE C 74 N LEU C 59 SHEET 3 B 6 CYS C 20 LEU C 27 1 N CYS C 20 O LYS C 71 SHEET 4 B 6 ALA C 96 ASP C 102 1 O VAL C 100 N LEU C 27 SHEET 5 B 6 VAL C 128 ASN C 134 1 O ASN C 134 N TYR C 101 SHEET 6 B 6 LEU C 159 GLU C 162 1 O LEU C 159 N LEU C 131 LINK OG SER A 35 MG MG A 601 1555 1555 2.17 LINK MG MG A 601 O2B GDP A 700 1555 1555 2.19 LINK MG MG A 601 O HOH A 706 1555 1555 2.21 LINK MG MG A 601 O HOH A 709 1555 1555 2.22 LINK MG MG A 601 O HOH A 718 1555 1555 2.21 LINK MG MG A 601 O HOH A 724 1555 1555 2.20 LINK OG SER C 35 MG MG C 800 1555 1555 2.31 LINK MG MG C 800 O2B GDP C 900 1555 1555 2.11 LINK MG MG C 800 O HOH C 907 1555 1555 2.04 LINK MG MG C 800 O HOH C 913 1555 1555 2.10 LINK MG MG C 800 O HOH C 916 1555 1555 2.02 LINK MG MG C 800 O HOH C 923 1555 1555 2.01 SITE 1 AC1 12 SER A 30 LYS A 34 ALA A 78 GLY A 79 SITE 2 AC1 12 LEU A 80 GLU A 81 HOH A 702 HOH A 703 SITE 3 AC1 12 HOH A 704 HOH A 706 HOH A 760 ASN C 172 SITE 1 AC2 6 SER A 35 GDP A 700 HOH A 706 HOH A 709 SITE 2 AC2 6 HOH A 718 HOH A 724 SITE 1 AC3 6 SER C 35 GDP C 900 HOH C 907 HOH C 913 SITE 2 AC3 6 HOH C 916 HOH C 923 SITE 1 AC4 25 ALA A 31 VAL A 32 GLY A 33 LYS A 34 SITE 2 AC4 25 SER A 35 SER A 36 PHE A 46 HIS A 47 SITE 3 AC4 25 GLU A 48 GLN A 50 ASN A 134 LYS A 135 SITE 4 AC4 25 ASP A 137 LEU A 138 SER A 164 ALA A 165 SITE 5 AC4 25 LYS A 166 MG A 601 HOH A 706 HOH A 708 SITE 6 AC4 25 HOH A 716 HOH A 718 HOH A 736 HOH A 752 SITE 7 AC4 25 THR C 167 SITE 1 AC5 22 ALA C 31 VAL C 32 GLY C 33 LYS C 34 SITE 2 AC5 22 SER C 35 SER C 36 PHE C 46 GLU C 48 SITE 3 AC5 22 ASN C 134 LYS C 135 ASP C 137 LEU C 138 SITE 4 AC5 22 SER C 164 ALA C 165 LYS C 166 MG C 800 SITE 5 AC5 22 HOH C 907 HOH C 916 HOH C 923 HOH C 933 SITE 6 AC5 22 HOH C 945 HOH C 984 CRYST1 38.401 70.931 137.610 90.00 90.00 90.00 P 21 21 21 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 0.026041 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014098 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007267 0.00000