PDB Short entry for 3M8D HEADER TRANSPORT PROTEIN 17-MAR-10 3M8D TITLE CRYSTAL STRUCTURE OF SPIN-LABELED BTUB V10R1 WITH BOUND CALCIUM AND TITLE 2 CYANOCOBALAMIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN B12 TRANSPORTER BTUB; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: BTUB, BFE, CER, DCRC, B3966, JW3938; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA BARREL, R1, SPIN LABEL, CELL MEMBRANE, CELL OUTER MEMBRANE, ION KEYWDS 2 TRANSPORT, MEMBRANE, METAL-BINDING, PHAGE RECOGNITION, PORIN, KEYWDS 3 RECEPTOR, TONB BOX, TRANSMEMBRANE, TRANSPORT, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.M.FREED,P.S.HORANYI,M.C.WIENER,D.S.CAFISO REVDAT 7 18-AUG-21 3M8D 1 COMPND HETNAM FORMUL LINK REVDAT 6 08-NOV-17 3M8D 1 REMARK REVDAT 5 15-FEB-12 3M8D 1 HET HETNAM HETATM LINK REVDAT 5 2 1 REMARK SEQADV SEQRES SITE REVDAT 4 26-OCT-11 3M8D 1 JRNL REVDAT 3 27-JUL-11 3M8D 1 REMARK REVDAT REVDAT 2 13-JUL-11 3M8D 1 VERSN REVDAT 1 15-SEP-10 3M8D 0 JRNL AUTH D.M.FREED,P.S.HORANYI,M.C.WIENER,D.S.CAFISO JRNL TITL CONFORMATIONAL EXCHANGE IN A MEMBRANE TRANSPORT PROTEIN IS JRNL TITL 2 ALTERED IN PROTEIN CRYSTALS. JRNL REF BIOPHYS.J. V. 99 1604 2010 JRNL REFN ISSN 0006-3495 JRNL PMID 20816073 JRNL DOI 10.1016/J.BPJ.2010.06.026 REMARK 2 REMARK 2 RESOLUTION. 2.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 32289 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) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1647 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) : 2.44 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1556 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.3610 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.3850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4552 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 234 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.01000 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): 0.375 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.275 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.192 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.249 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4901 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3271 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6660 ; 2.037 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7884 ; 0.969 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 581 ; 9.025 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 234 ;35.674 ;23.803 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 681 ;14.350 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;21.720 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 688 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5483 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1046 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2864 ; 0.899 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1212 ; 0.186 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4584 ; 1.645 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2037 ; 2.514 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2076 ; 4.014 ; 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 132 REMARK 3 ORIGIN FOR THE GROUP (A): 21.5576 -27.7695 -24.2165 REMARK 3 T TENSOR REMARK 3 T11: 0.0819 T22: 0.4348 REMARK 3 T33: 0.2050 T12: 0.0270 REMARK 3 T13: -0.0472 T23: 0.1560 REMARK 3 L TENSOR REMARK 3 L11: 1.5059 L22: 1.8189 REMARK 3 L33: 2.5488 L12: -0.3301 REMARK 3 L13: -0.6467 L23: -0.7960 REMARK 3 S TENSOR REMARK 3 S11: -0.1152 S12: -0.1671 S13: 0.0615 REMARK 3 S21: 0.3693 S22: 0.0687 S23: -0.1509 REMARK 3 S31: -0.1943 S32: 0.1370 S33: 0.0465 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 : A 137 A 594 REMARK 3 ORIGIN FOR THE GROUP (A): 20.8979 -29.3190 -19.8176 REMARK 3 T TENSOR REMARK 3 T11: 0.1168 T22: 0.4116 REMARK 3 T33: 0.2008 T12: 0.0574 REMARK 3 T13: -0.0307 T23: 0.1705 REMARK 3 L TENSOR REMARK 3 L11: 1.0934 L22: 1.0818 REMARK 3 L33: 1.0196 L12: -0.0173 REMARK 3 L13: -0.0838 L23: -0.1247 REMARK 3 S TENSOR REMARK 3 S11: -0.1201 S12: -0.1559 S13: 0.1049 REMARK 3 S21: 0.2905 S22: 0.0921 S23: -0.0855 REMARK 3 S31: -0.1838 S32: 0.0271 S33: 0.0280 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 3M8D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000058236. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SI 220. ROSENBAUM-ROCK DOUBLE REMARK 200 -CRYSTAL MONOCHROMATOR: LIQUID REMARK 200 NITROGEN COOLED; SAGITALLY REMARK 200 FOCUSING 2ND CRYSTAL, ROSENBAUM- REMARK 200 ROCK VERTICAL FOCUSING MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32358 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.440 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.12100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.45800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHASER 2.1.4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5% PEG3350, 150 MM CALCIUM CHLORIDE, REMARK 280 20 MM BIS TRIS, 10 MM C8E4, PH 6.6, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 74.81900 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 149.63800 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 149.63800 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 74.81900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLN A 1 REMARK 465 ASP A 2 REMARK 465 THR A 3 REMARK 465 SER A 4 REMARK 465 PRO A 5 REMARK 465 ASP A 6 REMARK 465 GLY A 325 REMARK 465 THR A 326 REMARK 465 GLY A 327 REMARK 465 TYR A 328 REMARK 465 VAL A 329 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 16 CG CD OE1 OE2 REMARK 470 VAL A 90 CB CG1 CG2 REMARK 470 LEU A 160 CD1 CD2 REMARK 470 ASP A 162 CB CG OD1 OD2 REMARK 470 LYS A 163 CG CD CE NZ REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 ARG A 226 NH1 NH2 REMARK 470 LYS A 244 CD CE NZ REMARK 470 GLN A 248 CG CD OE1 NE2 REMARK 470 GLU A 259 CG CD OE1 OE2 REMARK 470 TYR A 281 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 281 OH REMARK 470 GLU A 330 N REMARK 470 GLN A 335 OE1 REMARK 470 PHE A 404 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 414 CE NZ REMARK 470 PHE A 422 CD1 CE1 REMARK 470 ASP A 448 OD1 OD2 REMARK 470 HIS A 449 CB CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 452 CD CE NZ REMARK 470 LEU A 511 CD1 CD2 REMARK 470 GLN A 537 CD OE1 NE2 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 GLY A 473 N GLY A 473 CA 0.098 REMARK 500 GLN A 580 CD GLN A 580 OE1 0.161 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 VAL A 306 CB - CA - C ANGL. DEV. = -12.3 DEGREES REMARK 500 GLY A 473 C - N - CA ANGL. DEV. = -13.2 DEGREES REMARK 500 PRO A 535 C - N - CD ANGL. DEV. = -21.4 DEGREES 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 ARG A 14 -13.59 76.77 REMARK 500 VAL A 90 -11.78 93.05 REMARK 500 ARG A 114 29.94 -155.77 REMARK 500 ASP A 121 -14.46 87.17 REMARK 500 ILE A 123 -64.83 -90.99 REMARK 500 GLU A 135 90.41 -162.37 REMARK 500 SER A 146 153.49 -47.84 REMARK 500 LYS A 163 6.12 81.41 REMARK 500 VAL A 181 -54.14 77.43 REMARK 500 ASP A 193 152.23 -48.95 REMARK 500 TYR A 281 75.96 43.86 REMARK 500 ARG A 283 -51.16 91.31 REMARK 500 ASP A 285 149.18 177.97 REMARK 500 TYR A 333 -22.70 96.44 REMARK 500 GLU A 456 -25.02 -158.19 REMARK 500 THR A 472 -69.86 -109.61 REMARK 500 TYR A 512 -139.90 58.24 REMARK 500 PRO A 535 137.32 -19.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TYR A 534 PRO A 535 -68.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 TYR A 534 -12.26 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 CA A 709 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 179 OD1 REMARK 620 2 GLN A 191 O 75.4 REMARK 620 3 ASP A 193 OD1 156.9 95.6 REMARK 620 4 ASP A 193 O 87.9 111.5 75.5 REMARK 620 5 ASP A 195 OD2 90.0 154.0 105.4 88.9 REMARK 620 6 ASP A 230 OD2 81.4 75.7 117.5 165.2 80.9 REMARK 620 7 ASP A 230 OD1 132.6 99.1 69.2 135.0 74.9 52.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 710 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 193 OD2 REMARK 620 2 ASP A 193 OD1 46.8 REMARK 620 3 ASP A 195 OD1 91.1 67.0 REMARK 620 4 TYR A 229 O 170.5 142.6 95.0 REMARK 620 5 ASP A 230 OD1 112.2 66.4 70.3 76.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3M8B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SPIN-LABELED BTUB V10R1 IN THE APO STATE DBREF 3M8D A 1 594 UNP P06129 BTUB_ECOLI 21 614 SEQRES 1 A 594 GLN ASP THR SER PRO ASP THR LEU VAL CYS THR ALA ASN SEQRES 2 A 594 ARG PHE GLU GLN PRO ARG SER THR VAL LEU ALA PRO THR SEQRES 3 A 594 THR VAL VAL THR ARG GLN ASP ILE ASP ARG TRP GLN SER SEQRES 4 A 594 THR SER VAL ASN ASP VAL LEU ARG ARG LEU PRO GLY VAL SEQRES 5 A 594 ASP ILE THR GLN ASN GLY GLY SER GLY GLN LEU SER SER SEQRES 6 A 594 ILE PHE ILE ARG GLY THR ASN ALA SER HIS VAL LEU VAL SEQRES 7 A 594 LEU ILE ASP GLY VAL ARG LEU ASN LEU ALA GLY VAL SER SEQRES 8 A 594 GLY SER ALA ASP LEU SER GLN PHE PRO ILE ALA LEU VAL SEQRES 9 A 594 GLN ARG VAL GLU TYR ILE ARG GLY PRO ARG SER ALA VAL SEQRES 10 A 594 TYR GLY SER ASP ALA ILE GLY GLY VAL VAL ASN ILE ILE SEQRES 11 A 594 THR THR ARG ASP GLU PRO GLY THR GLU ILE SER ALA GLY SEQRES 12 A 594 TRP GLY SER ASN SER TYR GLN ASN TYR ASP VAL SER THR SEQRES 13 A 594 GLN GLN GLN LEU GLY ASP LYS THR ARG VAL THR LEU LEU SEQRES 14 A 594 GLY ASP TYR ALA HIS THR HIS GLY TYR ASP VAL VAL ALA SEQRES 15 A 594 TYR GLY ASN THR GLY THR GLN ALA GLN THR ASP ASN ASP SEQRES 16 A 594 GLY PHE LEU SER LYS THR LEU TYR GLY ALA LEU GLU HIS SEQRES 17 A 594 ASN PHE THR ASP ALA TRP SER GLY PHE VAL ARG GLY TYR SEQRES 18 A 594 GLY TYR ASP ASN ARG THR ASN TYR ASP ALA TYR TYR SER SEQRES 19 A 594 PRO GLY SER PRO LEU LEU ASP THR ARG LYS LEU TYR SER SEQRES 20 A 594 GLN SER TRP ASP ALA GLY LEU ARG TYR ASN GLY GLU LEU SEQRES 21 A 594 ILE LYS SER GLN LEU ILE THR SER TYR SER HIS SER LYS SEQRES 22 A 594 ASP TYR ASN TYR ASP PRO HIS TYR GLY ARG TYR ASP SER SEQRES 23 A 594 SER ALA THR LEU ASP GLU MET LYS GLN TYR THR VAL GLN SEQRES 24 A 594 TRP ALA ASN ASN VAL ILE VAL GLY HIS GLY SER ILE GLY SEQRES 25 A 594 ALA GLY VAL ASP TRP GLN LYS GLN THR THR THR PRO GLY SEQRES 26 A 594 THR GLY TYR VAL GLU ASP GLY TYR ASP GLN ARG ASN THR SEQRES 27 A 594 GLY ILE TYR LEU THR GLY LEU GLN GLN VAL GLY ASP PHE SEQRES 28 A 594 THR PHE GLU GLY ALA ALA ARG SER ASP ASP ASN SER GLN SEQRES 29 A 594 PHE GLY ARG HIS GLY THR TRP GLN THR SER ALA GLY TRP SEQRES 30 A 594 GLU PHE ILE GLU GLY TYR ARG PHE ILE ALA SER TYR GLY SEQRES 31 A 594 THR SER TYR LYS ALA PRO ASN LEU GLY GLN LEU TYR GLY SEQRES 32 A 594 PHE TYR GLY ASN PRO ASN LEU ASP PRO GLU LYS SER LYS SEQRES 33 A 594 GLN TRP GLU GLY ALA PHE GLU GLY LEU THR ALA GLY VAL SEQRES 34 A 594 ASN TRP ARG ILE SER GLY TYR ARG ASN ASP VAL SER ASP SEQRES 35 A 594 LEU ILE ASP TYR ASP ASP HIS THR LEU LYS TYR TYR ASN SEQRES 36 A 594 GLU GLY LYS ALA ARG ILE LYS GLY VAL GLU ALA THR ALA SEQRES 37 A 594 ASN PHE ASP THR GLY PRO LEU THR HIS THR VAL SER TYR SEQRES 38 A 594 ASP TYR VAL ASP ALA ARG ASN ALA ILE THR ASP THR PRO SEQRES 39 A 594 LEU LEU ARG ARG ALA LYS GLN GLN VAL LYS TYR GLN LEU SEQRES 40 A 594 ASP TRP GLN LEU TYR ASP PHE ASP TRP GLY ILE THR TYR SEQRES 41 A 594 GLN TYR LEU GLY THR ARG TYR ASP LYS ASP TYR SER SER SEQRES 42 A 594 TYR PRO TYR GLN THR VAL LYS MET GLY GLY VAL SER LEU SEQRES 43 A 594 TRP ASP LEU ALA VAL ALA TYR PRO VAL THR SER HIS LEU SEQRES 44 A 594 THR VAL ARG GLY LYS ILE ALA ASN LEU PHE ASP LYS ASP SEQRES 45 A 594 TYR GLU THR VAL TYR GLY TYR GLN THR ALA GLY ARG GLU SEQRES 46 A 594 TYR THR LEU SER GLY SER TYR THR PHE HET CNC A 701 93 HET C8E A 702 21 HET C8E A 703 21 HET C8E A 704 21 HET C8E A 705 21 HET C8E A 706 21 HET C8E A 707 21 HET MTN A 708 12 HET CA A 709 1 HET CA A 710 1 HET CA A 711 1 HETNAM CNC CYANOCOBALAMIN HETNAM C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE HETNAM MTN S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3- HETNAM 2 MTN YL)METHYL] METHANESULFONOTHIOATE HETNAM CA CALCIUM ION HETSYN MTN MTSL FORMUL 2 CNC C63 H89 CO N14 O14 P 2+ FORMUL 3 C8E 6(C16 H34 O5) FORMUL 9 MTN C10 H18 N O3 S2 FORMUL 10 CA 3(CA 2+) FORMUL 13 HOH *76(H2 O) HELIX 1 1 SER A 20 VAL A 22 5 3 HELIX 2 2 ARG A 31 GLN A 38 1 8 HELIX 3 3 SER A 41 ARG A 47 1 7 HELIX 4 4 ASN A 72 SER A 74 5 3 HELIX 5 5 ASP A 95 PHE A 99 5 5 HELIX 6 6 PRO A 100 VAL A 104 5 5 HELIX 7 7 ARG A 114 GLY A 119 1 6 HELIX 8 8 ASN A 397 GLY A 403 1 7 HELIX 9 9 ASP A 448 LEU A 451 5 4 SHEET 1 A 2 LEU A 8 VAL A 9 0 SHEET 2 A 2 GLN A 17 PRO A 18 -1 O GLN A 17 N VAL A 9 SHEET 1 B 5 THR A 26 THR A 30 0 SHEET 2 B 5 ARG A 106 ARG A 111 -1 O VAL A 107 N VAL A 29 SHEET 3 B 5 GLY A 125 ILE A 130 -1 O ASN A 128 N GLU A 108 SHEET 4 B 5 VAL A 76 ILE A 80 1 N LEU A 79 O VAL A 127 SHEET 5 B 5 VAL A 83 ARG A 84 -1 O VAL A 83 N ILE A 80 SHEET 1 C 2 VAL A 52 GLN A 56 0 SHEET 2 C 2 SER A 64 ILE A 68 -1 O SER A 65 N THR A 55 SHEET 1 D23 GLY A 137 GLY A 145 0 SHEET 2 D23 TYR A 149 GLN A 159 -1 O ASN A 151 N GLY A 143 SHEET 3 D23 THR A 164 THR A 175 -1 O HIS A 174 N GLN A 150 SHEET 4 D23 PHE A 197 ASN A 209 -1 O THR A 201 N ASP A 171 SHEET 5 D23 TRP A 214 ASN A 228 -1 O GLY A 220 N GLY A 204 SHEET 6 D23 THR A 242 ASN A 257 -1 O ASP A 251 N ARG A 219 SHEET 7 D23 ILE A 261 TYR A 277 -1 O THR A 267 N ALA A 252 SHEET 8 D23 THR A 289 ILE A 305 -1 O ASN A 303 N LYS A 262 SHEET 9 D23 GLY A 309 THR A 322 -1 O ALA A 313 N ASN A 302 SHEET 10 D23 ASP A 334 VAL A 348 -1 O THR A 343 N GLY A 312 SHEET 11 D23 PHE A 351 ASN A 362 -1 O SER A 359 N ILE A 340 SHEET 12 D23 GLY A 366 ILE A 380 -1 O GLY A 366 N ASN A 362 SHEET 13 D23 TYR A 383 LYS A 394 -1 O PHE A 385 N TRP A 377 SHEET 14 D23 GLU A 413 THR A 426 -1 O GLN A 417 N GLY A 390 SHEET 15 D23 VAL A 429 TYR A 446 -1 O TRP A 431 N GLY A 424 SHEET 16 D23 TYR A 453 ASP A 471 -1 O THR A 467 N ARG A 432 SHEET 17 D23 LEU A 475 ASN A 488 -1 O TYR A 483 N VAL A 464 SHEET 18 D23 GLN A 501 LEU A 511 -1 O ASP A 508 N THR A 476 SHEET 19 D23 PHE A 514 LEU A 523 -1 O TYR A 522 N VAL A 503 SHEET 20 D23 VAL A 544 PRO A 554 -1 O ALA A 550 N GLY A 517 SHEET 21 D23 LEU A 559 ALA A 566 -1 O GLY A 563 N VAL A 551 SHEET 22 D23 GLU A 585 THR A 593 -1 O SER A 589 N ARG A 562 SHEET 23 D23 GLY A 137 GLY A 145 -1 N ILE A 140 O TYR A 592 SHEET 1 E 2 ARG A 526 ASP A 530 0 SHEET 2 E 2 GLN A 537 MET A 541 -1 O MET A 541 N ARG A 526 LINK SG CYS A 10 S1 MTN A 708 1555 1555 2.02 LINK OD1 ASP A 179 CA CA A 709 1555 1555 2.24 LINK O GLN A 191 CA CA A 709 1555 1555 2.54 LINK OD1 ASP A 193 CA CA A 709 1555 1555 2.21 LINK O ASP A 193 CA CA A 709 1555 1555 2.46 LINK OD2 ASP A 193 CA CA A 710 1555 1555 2.50 LINK OD1 ASP A 193 CA CA A 710 1555 1555 2.90 LINK OD2 ASP A 195 CA CA A 709 1555 1555 2.60 LINK OD1 ASP A 195 CA CA A 710 1555 1555 2.41 LINK O TYR A 229 CA CA A 710 1555 1555 2.33 LINK OD2 ASP A 230 CA CA A 709 1555 1555 2.03 LINK OD1 ASP A 230 CA CA A 709 1555 1555 2.76 LINK OD1 ASP A 230 CA CA A 710 1555 1555 2.22 SITE 1 AC1 17 ASN A 57 GLN A 62 LEU A 63 SER A 65 SITE 2 AC1 17 PHE A 67 GLY A 89 SER A 91 SER A 93 SITE 3 AC1 17 ASN A 185 TYR A 229 ASP A 230 ASN A 276 SITE 4 AC1 17 THR A 289 ARG A 497 TYR A 531 TYR A 579 SITE 5 AC1 17 HOH A 842 SITE 1 AC2 8 ARG A 358 ARG A 367 THR A 370 PHE A 470 SITE 2 AC2 8 ASP A 471 THR A 472 GLY A 473 C8E A 704 SITE 1 AC3 7 TRP A 317 THR A 338 ASP A 361 SER A 363 SITE 2 AC3 7 TYR A 383 PHE A 422 TRP A 431 SITE 1 AC4 7 ILE A 261 ASN A 302 ALA A 313 ILE A 433 SITE 2 AC4 7 ALA A 466 THR A 467 C8E A 702 SITE 1 AC5 5 GLY A 344 LEU A 345 PHE A 353 GLY A 355 SITE 2 AC5 5 THR A 373 SITE 1 AC6 4 TYR A 256 GLY A 435 TYR A 436 GLY A 463 SITE 1 AC7 1 ALA A 357 SITE 1 AC8 5 ASP A 179 GLN A 191 ASP A 193 ASP A 195 SITE 2 AC8 5 ASP A 230 SITE 1 AC9 4 ASP A 193 ASP A 195 TYR A 229 ASP A 230 SITE 1 BC1 2 HIS A 174 HIS A 176 CRYST1 82.051 82.051 224.457 90.00 90.00 120.00 P 31 2 1 6 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 0.012188 0.007036 0.000000 0.00000 SCALE2 0.000000 0.014073 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004455 0.00000