PDB Short entry for 1YZK HEADER PROTEIN TRANSPORT 28-FEB-05 1YZK TITLE GPPNHP BOUND RAB11 GTPASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-11A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RAB-11, YL8; COMPND 5 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: RAB11A, RAB11; 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: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET15B KEYWDS RAB GTPASE, RAB11, VESICULAR TRAFFICKING, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.EATHIRAJ,X.PAN,C.RITACCO,D.G.LAMBRIGHT REVDAT 5 03-APR-24 1YZK 1 REMARK REVDAT 4 14-FEB-24 1YZK 1 REMARK SEQADV LINK REVDAT 3 31-JAN-18 1YZK 1 REMARK REVDAT 2 24-FEB-09 1YZK 1 VERSN REVDAT 1 26-JUL-05 1YZK 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 12992 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 697 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 837 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.14 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE SET COUNT : 45 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1309 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 219 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.30000 REMARK 3 B22 (A**2) : -0.30000 REMARK 3 B33 (A**2) : 0.60000 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): 0.174 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.161 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.105 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.692 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1365 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1241 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1859 ; 1.067 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2855 ; 0.723 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 167 ; 5.213 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 61 ;32.010 ;23.115 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 220 ;11.381 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;13.849 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 215 ; 0.056 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1508 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 293 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 268 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1240 ; 0.170 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 665 ; 0.174 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 797 ; 0.077 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 152 ; 0.155 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.062 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 1 ; 0.139 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 33 ; 0.294 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 34 ; 0.188 ; 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): 1084 ; 0.686 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 347 ; 0.081 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1328 ; 0.723 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 644 ; 1.196 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 531 ; 1.782 ; 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 1YZK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032109. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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 : CONFOCAL BLUE OPTIC DEVICE REMARK 200 OPTICS : NULL 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 : 14293 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 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) : 0.25200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.600 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 RAB5C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NACL, GLYCEROL, MES, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 4K, TEMPERATURE 277.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 36.97300 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 36.97300 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 74.09850 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 36.97300 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 36.97300 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 74.09850 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 36.97300 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 36.97300 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 74.09850 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 36.97300 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 36.97300 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 74.09850 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 36.97300 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 36.97300 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 74.09850 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 36.97300 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 36.97300 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 74.09850 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 36.97300 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 36.97300 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 74.09850 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 36.97300 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 36.97300 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 74.09850 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: 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 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 MET A -8 REMARK 465 GLY A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 LEU A 2 REMARK 465 VAL A 3 REMARK 465 PRO A 4 REMARK 465 ARG A 5 REMARK 465 GLY A 6 REMARK 465 SER A 7 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 GLU A 35 CG CD OE1 OE2 REMARK 470 LYS A 41 CG CD CE NZ REMARK 470 GLU A 103 CG CD OE1 OE2 REMARK 470 ARG A 129 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 144 CG CD OE1 OE2 REMARK 470 LYS A 145 CG CD CE NZ REMARK 470 GLU A 162 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 255 O HOH A 268 5555 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 LYS A 125 37.82 72.21 REMARK 500 LEU A 128 35.57 -93.13 REMARK 500 SER A 158 -5.94 79.15 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 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 25 OG REMARK 620 2 THR A 43 OG1 77.4 REMARK 620 3 GNP A 200 O2G 169.8 92.4 REMARK 620 4 GNP A 200 O2B 89.6 167.0 100.7 REMARK 620 5 HOH A 216 O 90.0 86.0 89.3 94.4 REMARK 620 6 HOH A 231 O 86.7 91.9 93.7 87.0 176.4 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP A 200 DBREF 1YZK A 8 175 UNP P62491 RB11A_HUMAN 8 175 SEQADV 1YZK MET A -8 UNP P62491 CLONING ARTIFACT SEQADV 1YZK GLY A -7 UNP P62491 CLONING ARTIFACT SEQADV 1YZK HIS A -6 UNP P62491 CLONING ARTIFACT SEQADV 1YZK HIS A -5 UNP P62491 CLONING ARTIFACT SEQADV 1YZK HIS A -4 UNP P62491 CLONING ARTIFACT SEQADV 1YZK HIS A -3 UNP P62491 CLONING ARTIFACT SEQADV 1YZK HIS A -2 UNP P62491 CLONING ARTIFACT SEQADV 1YZK HIS A -1 UNP P62491 CLONING ARTIFACT SEQADV 1YZK GLY A 0 UNP P62491 CLONING ARTIFACT SEQADV 1YZK SER A 1 UNP P62491 CLONING ARTIFACT SEQADV 1YZK LEU A 2 UNP P62491 CLONING ARTIFACT SEQADV 1YZK VAL A 3 UNP P62491 CLONING ARTIFACT SEQADV 1YZK PRO A 4 UNP P62491 CLONING ARTIFACT SEQADV 1YZK ARG A 5 UNP P62491 CLONING ARTIFACT SEQADV 1YZK GLY A 6 UNP P62491 CLONING ARTIFACT SEQADV 1YZK SER A 7 UNP P62491 CLONING ARTIFACT SEQRES 1 A 184 MET GLY HIS HIS HIS HIS HIS HIS GLY SER LEU VAL PRO SEQRES 2 A 184 ARG GLY SER TYR ASP TYR LEU PHE LYS VAL VAL LEU ILE SEQRES 3 A 184 GLY ASP SER GLY VAL GLY LYS SER ASN LEU LEU SER ARG SEQRES 4 A 184 PHE THR ARG ASN GLU PHE ASN LEU GLU SER LYS SER THR SEQRES 5 A 184 ILE GLY VAL GLU PHE ALA THR ARG SER ILE GLN VAL ASP SEQRES 6 A 184 GLY LYS THR ILE LYS ALA GLN ILE TRP ASP THR ALA GLY SEQRES 7 A 184 GLN GLU ARG TYR ARG ALA ILE THR SER ALA TYR TYR ARG SEQRES 8 A 184 GLY ALA VAL GLY ALA LEU LEU VAL TYR ASP ILE ALA LYS SEQRES 9 A 184 HIS LEU THR TYR GLU ASN VAL GLU ARG TRP LEU LYS GLU SEQRES 10 A 184 LEU ARG ASP HIS ALA ASP SER ASN ILE VAL ILE MET LEU SEQRES 11 A 184 VAL GLY ASN LYS SER ASP LEU ARG HIS LEU ARG ALA VAL SEQRES 12 A 184 PRO THR ASP GLU ALA ARG ALA PHE ALA GLU LYS ASN GLY SEQRES 13 A 184 LEU SER PHE ILE GLU THR SER ALA LEU ASP SER THR ASN SEQRES 14 A 184 VAL GLU ALA ALA PHE GLN THR ILE LEU THR GLU ILE TYR SEQRES 15 A 184 ARG ILE HET MG A 201 1 HET GNP A 200 32 HETNAM MG MAGNESIUM ION HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER FORMUL 2 MG MG 2+ FORMUL 3 GNP C10 H17 N6 O13 P3 FORMUL 4 HOH *219(H2 O) HELIX 1 1 GLY A 23 ASN A 34 1 12 HELIX 2 2 THR A 77 ARG A 82 1 6 HELIX 3 3 LYS A 95 ASN A 101 1 7 HELIX 4 4 ASN A 101 ALA A 113 1 13 HELIX 5 5 LYS A 125 ARG A 132 5 8 HELIX 6 6 PRO A 135 ASN A 146 1 12 HELIX 7 7 ASN A 160 ILE A 175 1 16 SHEET 1 A 6 VAL A 46 VAL A 55 0 SHEET 2 A 6 LYS A 58 THR A 67 -1 O ILE A 60 N ILE A 53 SHEET 3 A 6 TYR A 10 ILE A 17 1 N VAL A 14 O TRP A 65 SHEET 4 A 6 ALA A 84 ASP A 92 1 O VAL A 90 N ILE A 17 SHEET 5 A 6 VAL A 118 ASN A 124 1 O VAL A 122 N LEU A 89 SHEET 6 A 6 SER A 149 GLU A 152 1 O SER A 149 N LEU A 121 LINK OG SER A 25 MG MG A 201 1555 1555 2.11 LINK OG1 THR A 43 MG MG A 201 1555 1555 2.17 LINK O2G GNP A 200 MG MG A 201 1555 1555 1.93 LINK O2B GNP A 200 MG MG A 201 1555 1555 2.00 LINK MG MG A 201 O HOH A 216 1555 1555 2.10 LINK MG MG A 201 O HOH A 231 1555 1555 2.16 SITE 1 AC1 5 SER A 25 THR A 43 GNP A 200 HOH A 216 SITE 2 AC1 5 HOH A 231 SITE 1 AC2 31 SER A 20 GLY A 21 VAL A 22 GLY A 23 SITE 2 AC2 31 LYS A 24 SER A 25 ASN A 26 PHE A 36 SITE 3 AC2 31 ASN A 37 LEU A 38 SER A 40 SER A 42 SITE 4 AC2 31 THR A 43 ALA A 68 GLY A 69 ASN A 124 SITE 5 AC2 31 LYS A 125 ASP A 127 LEU A 128 SER A 154 SITE 6 AC2 31 ALA A 155 LEU A 156 MG A 201 HOH A 216 SITE 7 AC2 31 HOH A 218 HOH A 231 HOH A 258 HOH A 273 SITE 8 AC2 31 HOH A 305 HOH A 359 HOH A 399 CRYST1 73.946 73.946 148.197 90.00 90.00 90.00 I 4 2 2 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 0.013523 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013523 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006748 0.00000