HEADER PROTEIN TRANSPORT 28-FEB-05 1YZU TITLE GPPNHP-BOUND RAB21 GTPASE AT 2.50 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-21; COMPND 3 CHAIN: A, B; COMPND 4 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: RAB21, KIAA0118; 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, RAB21, VESICULAR TRAFFICKING, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.EATHIRAJ,X.PAN,C.RITACCO,D.G.LAMBRIGHT REVDAT 4 03-APR-24 1YZU 1 REMARK REVDAT 3 14-FEB-24 1YZU 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1YZU 1 VERSN REVDAT 1 26-JUL-05 1YZU 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. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 13121 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 679 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 915 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE SET COUNT : 55 REMARK 3 BIN FREE R VALUE : 0.3620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2490 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 187 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 55.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.36000 REMARK 3 B22 (A**2) : 6.50000 REMARK 3 B33 (A**2) : -3.14000 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): 0.624 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.346 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.259 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.530 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.884 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2602 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2326 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3540 ; 1.420 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5390 ; 0.811 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 328 ; 6.420 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 106 ;35.517 ;24.528 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 413 ;15.936 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;22.495 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 404 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2891 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 518 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 630 ; 0.245 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2412 ; 0.195 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1238 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1538 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 193 ; 0.204 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.013 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.155 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 18 ; 0.230 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 58 ; 0.241 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.259 ; 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): 2092 ; 0.823 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 686 ; 0.105 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2570 ; 1.004 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1182 ; 1.321 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 970 ; 1.908 ; 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 1YZU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032119. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 : 13852 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 95.6 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38700 REMARK 200 FOR SHELL : 4.800 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: POLYALANINE RAB3A GTPASE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 4000, 10% GLYCEROL, 200MM NA REMARK 280 THIOCYANATE, 50MM MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-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 38.91700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.88000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.85950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.88000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.91700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.85950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 38.91700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.85950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 52.88000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.85950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.91700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 52.88000 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: 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 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 A 387 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 GLY A 14 REMARK 465 SER A 15 REMARK 465 ARG A 16 REMARK 465 GLU A 182 REMARK 465 THR A 183 REMARK 465 GLY B 14 REMARK 465 SER B 15 REMARK 465 ARG B 16 REMARK 465 GLU B 182 REMARK 465 THR B 183 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 LEU A 52 CG CD1 CD2 REMARK 470 LYS A 60 CG CD CE NZ REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 GLU A 79 CG CD OE1 OE2 REMARK 470 ARG A 80 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 87 CG1 CG2 CD1 REMARK 470 ARG A 90 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 111 CG CD CE NZ REMARK 470 LYS A 115 CG CD CE NZ REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 470 LYS A 119 CG CD CE NZ REMARK 470 GLU A 124 CG CD OE1 OE2 REMARK 470 LYS A 138 CG CD CE NZ REMARK 470 GLU A 139 CG CD OE1 OE2 REMARK 470 GLN A 145 CG CD OE1 NE2 REMARK 470 GLU A 152 CG CD OE1 OE2 REMARK 470 LYS A 157 CG CD CE NZ REMARK 470 LEU B 52 CG CD1 CD2 REMARK 470 LYS B 60 CG CD CE NZ REMARK 470 LYS B 66 CG CD CE NZ REMARK 470 GLU B 79 CG CD OE1 OE2 REMARK 470 ARG B 80 CG CD NE CZ NH1 NH2 REMARK 470 ILE B 87 CG1 CG2 CD1 REMARK 470 ARG B 90 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 111 CG CD CE NZ REMARK 470 LYS B 115 CG CD CE NZ REMARK 470 GLU B 116 CG CD OE1 OE2 REMARK 470 ARG B 118 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 119 CG CD CE NZ REMARK 470 MET B 120 CG SD CE REMARK 470 ASN B 123 CG OD1 ND2 REMARK 470 GLU B 124 CG CD OE1 OE2 REMARK 470 LYS B 138 CG CD CE NZ REMARK 470 GLU B 139 CG CD OE1 OE2 REMARK 470 GLN B 145 CG CD OE1 NE2 REMARK 470 GLU B 152 CG CD OE1 OE2 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 332 O HOH A 375 2.16 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 CYS A 29 -13.43 -34.48 REMARK 500 LYS A 133 48.10 81.63 REMARK 500 LEU A 136 42.59 -105.53 REMARK 500 MET B 120 2.12 -175.05 REMARK 500 ASN B 123 3.47 -38.05 REMARK 500 LYS B 133 34.75 82.50 REMARK 500 HIS B 141 27.30 -149.15 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 300 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 33 OG1 REMARK 620 2 THR A 51 OG1 81.3 REMARK 620 3 GNP A 301 O2G 170.7 91.5 REMARK 620 4 GNP A 301 O2B 92.8 173.8 94.6 REMARK 620 5 HOH A 305 O 81.7 83.9 91.7 97.0 REMARK 620 6 HOH A 320 O 86.7 84.3 98.5 93.6 164.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 400 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 33 OG1 REMARK 620 2 THR B 51 OG1 81.3 REMARK 620 3 GNP B 401 O2G 168.8 103.1 REMARK 620 4 GNP B 401 O2B 86.3 161.5 86.8 REMARK 620 5 HOH B 404 O 83.7 81.8 86.8 83.3 REMARK 620 6 HOH B 407 O 93.4 99.8 95.9 94.6 176.5 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 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP B 401 DBREF 1YZU A 16 183 UNP Q9UL25 RAB21_HUMAN 16 183 DBREF 1YZU B 16 183 UNP Q9UL25 RAB21_HUMAN 16 183 SEQADV 1YZU GLY A 14 UNP Q9UL25 CLONING ARTIFACT SEQADV 1YZU SER A 15 UNP Q9UL25 CLONING ARTIFACT SEQADV 1YZU GLY B 14 UNP Q9UL25 CLONING ARTIFACT SEQADV 1YZU SER B 15 UNP Q9UL25 CLONING ARTIFACT SEQRES 1 A 170 GLY SER ARG ALA TYR SER PHE LYS VAL VAL LEU LEU GLY SEQRES 2 A 170 GLU GLY CYS VAL GLY LYS THR SER LEU VAL LEU ARG TYR SEQRES 3 A 170 CYS GLU ASN LYS PHE ASN ASP LYS HIS ILE THR THR LEU SEQRES 4 A 170 GLN ALA SER PHE LEU THR LYS LYS LEU ASN ILE GLY GLY SEQRES 5 A 170 LYS ARG VAL ASN LEU ALA ILE TRP ASP THR ALA GLY GLN SEQRES 6 A 170 GLU ARG PHE HIS ALA LEU GLY PRO ILE TYR TYR ARG ASP SEQRES 7 A 170 SER ASN GLY ALA ILE LEU VAL TYR ASP ILE THR ASP GLU SEQRES 8 A 170 ASP SER PHE GLN LYS VAL LYS ASN TRP VAL LYS GLU LEU SEQRES 9 A 170 ARG LYS MET LEU GLY ASN GLU ILE CYS LEU CYS ILE VAL SEQRES 10 A 170 GLY ASN LYS ILE ASP LEU GLU LYS GLU ARG HIS VAL SER SEQRES 11 A 170 ILE GLN GLU ALA GLU SER TYR ALA GLU SER VAL GLY ALA SEQRES 12 A 170 LYS HIS TYR HIS THR SER ALA LYS GLN ASN LYS GLY ILE SEQRES 13 A 170 GLU GLU LEU PHE LEU ASP LEU CYS LYS ARG MET ILE GLU SEQRES 14 A 170 THR SEQRES 1 B 170 GLY SER ARG ALA TYR SER PHE LYS VAL VAL LEU LEU GLY SEQRES 2 B 170 GLU GLY CYS VAL GLY LYS THR SER LEU VAL LEU ARG TYR SEQRES 3 B 170 CYS GLU ASN LYS PHE ASN ASP LYS HIS ILE THR THR LEU SEQRES 4 B 170 GLN ALA SER PHE LEU THR LYS LYS LEU ASN ILE GLY GLY SEQRES 5 B 170 LYS ARG VAL ASN LEU ALA ILE TRP ASP THR ALA GLY GLN SEQRES 6 B 170 GLU ARG PHE HIS ALA LEU GLY PRO ILE TYR TYR ARG ASP SEQRES 7 B 170 SER ASN GLY ALA ILE LEU VAL TYR ASP ILE THR ASP GLU SEQRES 8 B 170 ASP SER PHE GLN LYS VAL LYS ASN TRP VAL LYS GLU LEU SEQRES 9 B 170 ARG LYS MET LEU GLY ASN GLU ILE CYS LEU CYS ILE VAL SEQRES 10 B 170 GLY ASN LYS ILE ASP LEU GLU LYS GLU ARG HIS VAL SER SEQRES 11 B 170 ILE GLN GLU ALA GLU SER TYR ALA GLU SER VAL GLY ALA SEQRES 12 B 170 LYS HIS TYR HIS THR SER ALA LYS GLN ASN LYS GLY ILE SEQRES 13 B 170 GLU GLU LEU PHE LEU ASP LEU CYS LYS ARG MET ILE GLU SEQRES 14 B 170 THR HET MG A 300 1 HET GNP A 301 32 HET MG B 400 1 HET GNP B 401 32 HETNAM MG MAGNESIUM ION HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER FORMUL 3 MG 2(MG 2+) FORMUL 4 GNP 2(C10 H17 N6 O13 P3) FORMUL 7 HOH *187(H2 O) HELIX 1 1 GLY A 28 VAL A 30 5 3 HELIX 2 2 GLY A 31 ASN A 42 1 12 HELIX 3 3 GLY A 77 TYR A 89 1 13 HELIX 4 4 ASP A 103 LYS A 119 1 17 HELIX 5 5 ILE A 134 ARG A 140 5 7 HELIX 6 6 SER A 143 SER A 153 1 11 HELIX 7 7 GLY A 168 ILE A 181 1 14 HELIX 8 8 GLY B 31 ASN B 42 1 12 HELIX 9 9 GLY B 77 TYR B 89 1 13 HELIX 10 10 ASP B 103 LYS B 109 1 7 HELIX 11 11 LYS B 109 LYS B 119 1 11 HELIX 12 12 ILE B 134 ARG B 140 5 7 HELIX 13 13 SER B 143 SER B 153 1 11 HELIX 14 14 GLY B 168 ILE B 181 1 14 SHEET 1 A 6 SER A 55 ILE A 63 0 SHEET 2 A 6 LYS A 66 ASP A 74 -1 O ILE A 72 N LEU A 57 SHEET 3 A 6 TYR A 18 GLY A 26 1 N TYR A 18 O ASN A 69 SHEET 4 A 6 GLY A 94 ASP A 100 1 O VAL A 98 N LEU A 25 SHEET 5 A 6 CYS A 126 ASN A 132 1 O VAL A 130 N LEU A 97 SHEET 6 A 6 LYS A 157 THR A 161 1 O THR A 161 N GLY A 131 SHEET 1 B 6 SER B 55 ILE B 63 0 SHEET 2 B 6 LYS B 66 ASP B 74 -1 O ILE B 72 N LEU B 57 SHEET 3 B 6 TYR B 18 LEU B 25 1 N TYR B 18 O ASN B 69 SHEET 4 B 6 GLY B 94 ASP B 100 1 O ILE B 96 N VAL B 23 SHEET 5 B 6 CYS B 126 ASN B 132 1 O VAL B 130 N LEU B 97 SHEET 6 B 6 LYS B 157 THR B 161 1 O TYR B 159 N GLY B 131 LINK OG1 THR A 33 MG MG A 300 1555 1555 2.25 LINK OG1 THR A 51 MG MG A 300 1555 1555 2.07 LINK MG MG A 300 O2G GNP A 301 1555 1555 1.76 LINK MG MG A 300 O2B GNP A 301 1555 1555 1.90 LINK MG MG A 300 O HOH A 305 1555 1555 2.04 LINK MG MG A 300 O HOH A 320 1555 1555 2.06 LINK OG1 THR B 33 MG MG B 400 1555 1555 1.96 LINK OG1 THR B 51 MG MG B 400 1555 1555 1.87 LINK MG MG B 400 O2G GNP B 401 1555 1555 1.79 LINK MG MG B 400 O2B GNP B 401 1555 1555 2.05 LINK MG MG B 400 O HOH B 404 1555 1555 2.23 LINK MG MG B 400 O HOH B 407 1555 1555 2.13 SITE 1 AC1 5 THR A 33 THR A 51 GNP A 301 HOH A 305 SITE 2 AC1 5 HOH A 320 SITE 1 AC2 5 THR B 33 THR B 51 GNP B 401 HOH B 404 SITE 2 AC2 5 HOH B 407 SITE 1 AC3 28 GLY A 28 CYS A 29 VAL A 30 GLY A 31 SITE 2 AC3 28 LYS A 32 THR A 33 SER A 34 PHE A 44 SITE 3 AC3 28 ASN A 45 ASP A 46 HIS A 48 THR A 50 SITE 4 AC3 28 THR A 51 ASN A 132 LYS A 133 ASP A 135 SITE 5 AC3 28 LEU A 136 SER A 162 ALA A 163 LYS A 164 SITE 6 AC3 28 MG A 300 HOH A 304 HOH A 305 HOH A 320 SITE 7 AC3 28 HOH A 334 HOH A 362 HOH A 372 HOH A 383 SITE 1 AC4 26 GLY B 28 CYS B 29 GLY B 31 LYS B 32 SITE 2 AC4 26 THR B 33 SER B 34 PHE B 44 ASN B 45 SITE 3 AC4 26 ASP B 46 HIS B 48 THR B 50 THR B 51 SITE 4 AC4 26 ASN B 132 LYS B 133 ASP B 135 LEU B 136 SITE 5 AC4 26 SER B 162 ALA B 163 LYS B 164 MG B 400 SITE 6 AC4 26 HOH B 404 HOH B 407 HOH B 413 HOH B 423 SITE 7 AC4 26 HOH B 427 HOH B 434 CRYST1 77.834 99.719 105.760 90.00 90.00 90.00 I 21 21 21 16 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 0.012848 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010028 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009455 0.00000