HEADER PROTEIN TRANSPORT 12-APR-10 3MJH TITLE CRYSTAL STRUCTURE OF HUMAN RAB5A IN COMPLEX WITH THE C2H2 ZINC FINGER TITLE 2 OF EEA1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-5A; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: RESIDUES 16-183; COMPND 5 EC: 3.6.5.2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: EARLY ENDOSOME ANTIGEN 1; COMPND 9 CHAIN: B, D; COMPND 10 FRAGMENT: C2H2-TYPE, RESIDUES 36-69; COMPND 11 SYNONYM: ENDOSOME-ASSOCIATED PROTEIN P162, ZINC FINGER FYVE DOMAIN- COMPND 12 CONTAINING PROTEIN 2; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RAB5, RAB5A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: K12, BL21 (DE3)CODON PLUS RIL CELLS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET15B, MODIFIED PET28A,PGEX; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: EARLY ENDOSOMAL ANTIGEN1(EEA1), EEA1, ZFYVE2; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: K12, BL21(DE3)CODON PLUS RIL CELLS; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET15B KEYWDS PROTEIN-ZINC FINGER COMPLEX, BETA BETA ALPHA FOLD, BETA HAIRPIN, KEYWDS 2 RAB5A GTPASE, EEA1, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR A.K.MISHRA,S.EATHIRAJ,D.G.LAMBRIGHT REVDAT 4 21-FEB-24 3MJH 1 REMARK REVDAT 3 06-OCT-21 3MJH 1 REMARK SEQADV LINK REVDAT 2 14-JUL-10 3MJH 1 JRNL REVDAT 1 05-MAY-10 3MJH 0 JRNL AUTH A.MISHRA,S.EATHIRAJ,S.CORVERA,D.G.LAMBRIGHT JRNL TITL STRUCTURAL BASIS FOR RAB GTPASE RECOGNITION AND ENDOSOME JRNL TITL 2 TETHERING BY THE C2H2 ZINC FINGER OF EARLY ENDOSOMAL JRNL TITL 3 AUTOANTIGEN 1 (EEA1). JRNL REF PROC.NATL.ACAD.SCI.USA V. 107 10866 2010 JRNL REFN ISSN 0027-8424 JRNL PMID 20534488 JRNL DOI 10.1073/PNAS.1000843107 REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0037 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) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 3 NUMBER OF REFLECTIONS : 21886 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1157 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) : 2.03 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1174 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 68 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3138 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 312 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.53000 REMARK 3 B22 (A**2) : -1.26000 REMARK 3 B33 (A**2) : -1.27000 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): 0.275 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.223 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.351 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3253 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4404 ; 1.203 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 398 ; 5.839 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 149 ;38.652 ;25.168 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 555 ;15.684 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;13.815 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 488 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2416 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1534 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2201 ; 0.299 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 261 ; 0.122 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.091 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 72 ; 0.217 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.218 ; 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): 2046 ; 0.608 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3184 ; 1.037 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1389 ; 1.417 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1220 ; 2.213 ; 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 : 1.20 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 3MJH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058621. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 5.0 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 : OSMIC MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27931 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04200 REMARK 200 FOR THE DATA SET : 44.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL 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: MOUSE RAB5C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 4000, 50MM SODIUM ACETATE, REMARK 280 0.2M SODIUM-POTASSIUM PHOSPHATE, 10% GLYCEROL, PH 5.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291.0K 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 23.20600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.74750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.19900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.74750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.20600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.19900 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 REMARK 350 TOTAL BURIED SURFACE AREA: 1210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 ASN C 16 REMARK 465 SER D 36 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 -1.65 72.21 REMARK 500 LEU A 137 39.23 -98.84 REMARK 500 SER A 167 1.35 95.16 REMARK 500 ASN B 68 -163.81 -163.27 REMARK 500 GLN C 121 72.27 -161.83 REMARK 500 ALA C 122 -177.22 -172.16 REMARK 500 LEU C 137 50.58 -97.09 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 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 34 OG REMARK 620 2 THR A 52 OG1 82.4 REMARK 620 3 GTP A 200 O2G 170.8 89.9 REMARK 620 4 GTP A 200 O2B 92.3 174.6 95.2 REMARK 620 5 HOH A 302 O 91.2 91.4 93.9 90.1 REMARK 620 6 HOH A 306 O 84.0 87.5 90.8 90.6 175.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 70 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 43 SG REMARK 620 2 CYS B 46 SG 119.8 REMARK 620 3 HIS B 59 NE2 105.3 111.3 REMARK 620 4 HIS B 64 NE2 96.2 117.7 104.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER C 34 OG REMARK 620 2 THR C 52 OG1 79.8 REMARK 620 3 GTP C 200 O2B 92.5 172.0 REMARK 620 4 GTP C 200 O2G 169.8 90.1 97.6 REMARK 620 5 HOH C 272 O 89.9 87.3 90.8 90.7 REMARK 620 6 HOH C 274 O 81.0 88.7 92.1 97.9 170.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 70 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 43 SG REMARK 620 2 CYS D 46 SG 117.0 REMARK 620 3 HIS D 59 NE2 103.4 109.5 REMARK 620 4 HIS D 64 NE2 103.4 112.6 110.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 70 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP C 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 70 DBREF 3MJH A 16 183 UNP P20339 RAB5A_HUMAN 16 183 DBREF 3MJH B 36 69 UNP Q15075 EEA1_HUMAN 36 69 DBREF 3MJH C 16 183 UNP P20339 RAB5A_HUMAN 16 183 DBREF 3MJH D 36 69 UNP Q15075 EEA1_HUMAN 36 69 SEQADV 3MJH LEU A 79 UNP P20339 GLN 79 ENGINEERED MUTATION SEQADV 3MJH LEU C 79 UNP P20339 GLN 79 ENGINEERED MUTATION SEQRES 1 A 168 ASN LYS ILE CYS GLN PHE LYS LEU VAL LEU LEU GLY GLU SEQRES 2 A 168 SER ALA VAL GLY LYS SER SER LEU VAL LEU ARG PHE VAL SEQRES 3 A 168 LYS GLY GLN PHE HIS GLU PHE GLN GLU SER THR ILE GLY SEQRES 4 A 168 ALA ALA PHE LEU THR GLN THR VAL CYS LEU ASP ASP THR SEQRES 5 A 168 THR VAL LYS PHE GLU ILE TRP ASP THR ALA GLY LEU GLU SEQRES 6 A 168 ARG TYR HIS SER LEU ALA PRO MET TYR TYR ARG GLY ALA SEQRES 7 A 168 GLN ALA ALA ILE VAL VAL TYR ASP ILE THR ASN GLU GLU SEQRES 8 A 168 SER PHE ALA ARG ALA LYS ASN TRP VAL LYS GLU LEU GLN SEQRES 9 A 168 ARG GLN ALA SER PRO ASN ILE VAL ILE ALA LEU SER GLY SEQRES 10 A 168 ASN LYS ALA ASP LEU ALA ASN LYS ARG ALA VAL ASP PHE SEQRES 11 A 168 GLN GLU ALA GLN SER TYR ALA ASP ASP ASN SER LEU LEU SEQRES 12 A 168 PHE MET GLU THR SER ALA LYS THR SER MET ASN VAL ASN SEQRES 13 A 168 GLU ILE PHE MET ALA ILE ALA LYS LYS LEU PRO LYS SEQRES 1 B 34 SER SER SER GLU GLY PHE ILE CYS PRO GLN CYS MET LYS SEQRES 2 B 34 SER LEU GLY SER ALA ASP GLU LEU PHE LYS HIS TYR GLU SEQRES 3 B 34 ALA VAL HIS ASP ALA GLY ASN ASP SEQRES 1 C 168 ASN LYS ILE CYS GLN PHE LYS LEU VAL LEU LEU GLY GLU SEQRES 2 C 168 SER ALA VAL GLY LYS SER SER LEU VAL LEU ARG PHE VAL SEQRES 3 C 168 LYS GLY GLN PHE HIS GLU PHE GLN GLU SER THR ILE GLY SEQRES 4 C 168 ALA ALA PHE LEU THR GLN THR VAL CYS LEU ASP ASP THR SEQRES 5 C 168 THR VAL LYS PHE GLU ILE TRP ASP THR ALA GLY LEU GLU SEQRES 6 C 168 ARG TYR HIS SER LEU ALA PRO MET TYR TYR ARG GLY ALA SEQRES 7 C 168 GLN ALA ALA ILE VAL VAL TYR ASP ILE THR ASN GLU GLU SEQRES 8 C 168 SER PHE ALA ARG ALA LYS ASN TRP VAL LYS GLU LEU GLN SEQRES 9 C 168 ARG GLN ALA SER PRO ASN ILE VAL ILE ALA LEU SER GLY SEQRES 10 C 168 ASN LYS ALA ASP LEU ALA ASN LYS ARG ALA VAL ASP PHE SEQRES 11 C 168 GLN GLU ALA GLN SER TYR ALA ASP ASP ASN SER LEU LEU SEQRES 12 C 168 PHE MET GLU THR SER ALA LYS THR SER MET ASN VAL ASN SEQRES 13 C 168 GLU ILE PHE MET ALA ILE ALA LYS LYS LEU PRO LYS SEQRES 1 D 34 SER SER SER GLU GLY PHE ILE CYS PRO GLN CYS MET LYS SEQRES 2 D 34 SER LEU GLY SER ALA ASP GLU LEU PHE LYS HIS TYR GLU SEQRES 3 D 34 ALA VAL HIS ASP ALA GLY ASN ASP HET GTP A 200 32 HET MG A 201 1 HET ZN B 70 1 HET GTP C 200 32 HET MG C 201 1 HET ZN D 70 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION FORMUL 5 GTP 2(C10 H16 N5 O14 P3) FORMUL 6 MG 2(MG 2+) FORMUL 7 ZN 2(ZN 2+) FORMUL 11 HOH *312(H2 O) HELIX 1 1 GLY A 32 GLY A 43 1 12 HELIX 2 2 LEU A 79 SER A 84 5 6 HELIX 3 3 LEU A 85 ARG A 91 1 7 HELIX 4 4 ASN A 104 ALA A 122 1 19 HELIX 5 5 LYS A 134 ARG A 141 5 8 HELIX 6 6 ASP A 144 ASP A 154 1 11 HELIX 7 7 ASN A 169 LEU A 181 1 13 HELIX 8 8 SER B 52 HIS B 64 1 13 HELIX 9 9 GLY C 32 GLY C 43 1 12 HELIX 10 10 LEU C 79 SER C 84 5 6 HELIX 11 11 LEU C 85 ARG C 91 1 7 HELIX 12 12 ASN C 104 GLN C 121 1 18 HELIX 13 13 LEU C 137 ARG C 141 5 5 HELIX 14 14 ASP C 144 ASN C 155 1 12 HELIX 15 15 ASN C 169 LEU C 181 1 13 HELIX 16 16 SER D 52 HIS D 64 1 13 SHEET 1 A 8 LEU A 158 GLU A 161 0 SHEET 2 A 8 VAL A 127 ASN A 133 1 N LEU A 130 O LEU A 158 SHEET 3 A 8 ALA A 95 ASP A 101 1 N ALA A 96 O ALA A 129 SHEET 4 A 8 LYS A 17 LEU A 26 1 N LEU A 26 O VAL A 99 SHEET 5 A 8 THR A 67 THR A 76 1 O LYS A 70 N CYS A 19 SHEET 6 A 8 ALA A 55 LEU A 64 -1 N LEU A 58 O ILE A 73 SHEET 7 A 8 GLU B 39 ILE B 42 -1 O GLY B 40 N ALA A 55 SHEET 8 A 8 SER B 49 LEU B 50 -1 O LEU B 50 N PHE B 41 SHEET 1 B 8 LEU C 158 GLU C 161 0 SHEET 2 B 8 VAL C 127 ASN C 133 1 N LEU C 130 O LEU C 158 SHEET 3 B 8 ALA C 95 ASP C 101 1 N ALA C 96 O ALA C 129 SHEET 4 B 8 ILE C 18 LEU C 26 1 N VAL C 24 O ILE C 97 SHEET 5 B 8 THR C 68 THR C 76 1 O GLU C 72 N LEU C 23 SHEET 6 B 8 ALA C 55 CYS C 63 -1 N LEU C 58 O ILE C 73 SHEET 7 B 8 GLU D 39 ILE D 42 -1 O GLY D 40 N ALA C 55 SHEET 8 B 8 SER D 49 LEU D 50 -1 O LEU D 50 N PHE D 41 LINK OG SER A 34 MG MG A 201 1555 1555 2.19 LINK OG1 THR A 52 MG MG A 201 1555 1555 2.03 LINK O2G GTP A 200 MG MG A 201 1555 1555 2.03 LINK O2B GTP A 200 MG MG A 201 1555 1555 2.10 LINK MG MG A 201 O HOH A 302 1555 1555 2.03 LINK MG MG A 201 O HOH A 306 1555 1555 2.31 LINK SG CYS B 43 ZN ZN B 70 1555 1555 2.27 LINK SG CYS B 46 ZN ZN B 70 1555 1555 2.28 LINK NE2 HIS B 59 ZN ZN B 70 1555 1555 2.05 LINK NE2 HIS B 64 ZN ZN B 70 1555 1555 2.26 LINK OG SER C 34 MG MG C 201 1555 1555 2.05 LINK OG1 THR C 52 MG MG C 201 1555 1555 2.25 LINK O2B GTP C 200 MG MG C 201 1555 1555 1.98 LINK O2G GTP C 200 MG MG C 201 1555 1555 2.05 LINK MG MG C 201 O HOH C 272 1555 1555 2.18 LINK MG MG C 201 O HOH C 274 1555 1555 2.10 LINK SG CYS D 43 ZN ZN D 70 1555 1555 2.32 LINK SG CYS D 46 ZN ZN D 70 1555 1555 2.43 LINK NE2 HIS D 59 ZN ZN D 70 1555 1555 1.96 LINK NE2 HIS D 64 ZN ZN D 70 1555 1555 2.07 SITE 1 AC1 26 HOH A 6 SER A 29 ALA A 30 VAL A 31 SITE 2 AC1 26 GLY A 32 LYS A 33 SER A 34 SER A 35 SITE 3 AC1 26 PHE A 45 HIS A 46 GLU A 47 GLN A 49 SITE 4 AC1 26 SER A 51 THR A 52 GLY A 78 ASN A 133 SITE 5 AC1 26 LYS A 134 ASP A 136 SER A 163 ALA A 164 SITE 6 AC1 26 LYS A 165 HOH A 196 MG A 201 HOH A 259 SITE 7 AC1 26 HOH A 302 HOH A 306 SITE 1 AC2 5 SER A 34 THR A 52 GTP A 200 HOH A 302 SITE 2 AC2 5 HOH A 306 SITE 1 AC3 4 CYS B 43 CYS B 46 HIS B 59 HIS B 64 SITE 1 AC4 26 HOH C 12 SER C 29 ALA C 30 VAL C 31 SITE 2 AC4 26 GLY C 32 LYS C 33 SER C 34 SER C 35 SITE 3 AC4 26 PHE C 45 HIS C 46 GLU C 47 GLN C 49 SITE 4 AC4 26 THR C 52 GLY C 78 ASN C 133 LYS C 134 SITE 5 AC4 26 ASP C 136 LEU C 137 SER C 163 ALA C 164 SITE 6 AC4 26 LYS C 165 HOH C 193 MG C 201 HOH C 272 SITE 7 AC4 26 HOH C 274 HOH C 306 SITE 1 AC5 5 SER C 34 THR C 52 GTP C 200 HOH C 272 SITE 2 AC5 5 HOH C 274 SITE 1 AC6 4 CYS D 43 CYS D 46 HIS D 59 HIS D 64 CRYST1 46.412 80.398 103.495 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 0.021546 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012438 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009662 0.00000