HEADER TRANSPORT PROTEIN 19-JUN-07 2V3P TITLE CRYSTALLOGRAPHIC ANALYSIS OF BETA-AXIAL LIGAND SUBSTITUTIONS IN TITLE 2 COBALAMIN BOUND TO TRANSCOBALAMIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCOBALAMIN-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TCII, TC II, TRANSCOBALAMIN II; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 ORGAN: BLOOD; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SMD 1168; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPICZ(ALPHA)-LB KEYWDS ION TRANSPORT, VITAMIN B12 TRANSPORT PROTEIN, TRANSPORT PROTEIN, BETA KEYWDS 2 LIGAND SUBSTITUTION EXPDTA X-RAY DIFFRACTION AUTHOR J.WUERGES,S.GEREMIA,L.RANDACCIO REVDAT 6 13-DEC-23 2V3P 1 REMARK REVDAT 5 31-OCT-12 2V3P 1 REMARK FORMUL REVDAT 4 13-JUL-11 2V3P 1 VERSN REVDAT 3 24-FEB-09 2V3P 1 VERSN REVDAT 2 15-APR-08 2V3P 1 REMARK HETATM CONECT MASTER REVDAT 1 30-OCT-07 2V3P 0 JRNL AUTH J.WUERGES,S.GEREMIA,S.N.FEDOSOV,L.RANDACCIO JRNL TITL VITAMIN B12 TRANSPORT PROTEINS: CRYSTALLOGRAPHIC ANALYSIS OF JRNL TITL 2 BETA-AXIAL LIGAND SUBSTITUTIONS IN COBALAMIN BOUND TO JRNL TITL 3 TRANSCOBALAMIN. JRNL REF IUBMB LIFE V. 59 722 2007 JRNL REFN ISSN 1521-6543 JRNL PMID 17943552 JRNL DOI 10.1080/15216540701673413 REMARK 2 REMARK 2 RESOLUTION. 2.90 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 16697 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) : 0.194 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.830 REMARK 3 FREE R VALUE TEST SET COUNT : 640 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1164 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3110 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.3500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3178 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 98 REMARK 3 SOLVENT ATOMS : 120 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 0.21000 REMARK 3 B12 (A**2) : -0.07000 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): 0.675 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.342 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.249 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 25.622 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.904 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3348 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4566 ; 1.333 ; 2.025 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 403 ; 5.995 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;39.457 ;23.776 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 586 ;18.612 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;20.797 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 506 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2512 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1561 ; 0.218 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2294 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 140 ; 0.139 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 32 ; 0.237 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.160 ; 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): 2067 ; 0.667 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3248 ; 1.158 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1415 ; 1.244 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1318 ; 2.208 ; 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 : 4 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 1 A 1 REMARK 3 ORIGIN FOR THE GROUP (A): 13.2434 37.9367 16.8046 REMARK 3 T TENSOR REMARK 3 T11: 0.1832 T22: -0.0376 REMARK 3 T33: 0.1021 T12: 0.0086 REMARK 3 T13: 0.0160 T23: -0.0790 REMARK 3 L TENSOR REMARK 3 L11: 5.6657 L22: 0.1210 REMARK 3 L33: 0.8131 L12: -0.8281 REMARK 3 L13: -2.1464 L23: 0.3137 REMARK 3 S TENSOR REMARK 3 S11: -0.0778 S12: 0.0625 S13: -0.6763 REMARK 3 S21: -0.1293 S22: 0.0845 S23: 0.3680 REMARK 3 S31: 0.5236 S32: -0.2907 S33: -0.0067 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 2 A 302 REMARK 3 ORIGIN FOR THE GROUP (A): 3.9545 47.6408 19.6303 REMARK 3 T TENSOR REMARK 3 T11: -0.0866 T22: -0.0445 REMARK 3 T33: -0.0520 T12: 0.0973 REMARK 3 T13: 0.0750 T23: -0.0468 REMARK 3 L TENSOR REMARK 3 L11: 1.7208 L22: 2.7071 REMARK 3 L33: 3.4763 L12: 0.1082 REMARK 3 L13: 0.6970 L23: 0.3812 REMARK 3 S TENSOR REMARK 3 S11: -0.0895 S12: 0.0668 S13: -0.0991 REMARK 3 S21: 0.1476 S22: -0.0577 S23: 0.2732 REMARK 3 S31: -0.0088 S32: -0.3186 S33: 0.1472 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 303 A 314 REMARK 3 ORIGIN FOR THE GROUP (A): 32.5704 46.2217 39.9966 REMARK 3 T TENSOR REMARK 3 T11: 0.7138 T22: 0.9632 REMARK 3 T33: 1.3143 T12: 0.5494 REMARK 3 T13: -0.0302 T23: -0.0302 REMARK 3 L TENSOR REMARK 3 L11: 27.3067 L22: 81.1208 REMARK 3 L33: 1.6574 L12: -46.3277 REMARK 3 L13: 2.9749 L23: -3.2132 REMARK 3 S TENSOR REMARK 3 S11: -3.4544 S12: -1.9941 S13: 3.1747 REMARK 3 S21: 4.6920 S22: 3.7904 S23: -1.8526 REMARK 3 S31: -0.1397 S32: -1.9716 S33: -0.3360 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 315 A 414 REMARK 3 ORIGIN FOR THE GROUP (A): 26.3767 31.2329 17.5864 REMARK 3 T TENSOR REMARK 3 T11: 0.0155 T22: -0.1189 REMARK 3 T33: -0.0521 T12: 0.0815 REMARK 3 T13: 0.0046 T23: -0.0208 REMARK 3 L TENSOR REMARK 3 L11: 4.1361 L22: 4.0394 REMARK 3 L33: 3.6510 L12: -1.3835 REMARK 3 L13: 0.0554 L23: 0.4002 REMARK 3 S TENSOR REMARK 3 S11: -0.1098 S12: 0.1402 S13: -0.1172 REMARK 3 S21: -0.0157 S22: -0.0238 S23: 0.1248 REMARK 3 S31: 0.1905 S32: 0.0374 S33: 0.1336 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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. AMINO ACIDS FROM LYS168 TO VAL176 WERE NOT MODELLED REMARK 3 DUE TO DISORDER. HIS175 AS UPPER AXIAL LIGAND OF COBALAMIN HAS REMARK 3 BEEN DISPLACED BY EXTERNALLY SUPPLIED SULFITE. REMARK 4 REMARK 4 2V3P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1290032965. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16711 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 29.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.66000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 2BBC REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE PROTEIN AT 0.5 MM IN 1 M NACL, 0.1 REMARK 280 M TRIS, PH 7.5 CRYSTALLIZED FROM 28% PEG 8000, 0.2 M MAGNESIUM REMARK 280 ACETATE, 0.1 M TRIS PH 8.5, 20% 2-METHYL-2, 4-PENTADIOL, 40 MM REMARK 280 (NH4)2SO3. 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 43.24733 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 86.49467 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 86.49467 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 43.24733 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 LYS A 168 REMARK 465 PRO A 169 REMARK 465 HIS A 170 REMARK 465 LEU A 171 REMARK 465 LEU A 172 REMARK 465 GLN A 173 REMARK 465 ASP A 174 REMARK 465 HIS A 175 REMARK 465 VAL A 176 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 ALA A 47 62.62 -105.97 REMARK 500 PRO A 69 171.31 -46.84 REMARK 500 ASP A 74 14.79 84.87 REMARK 500 ASP A 75 -45.72 -135.38 REMARK 500 ASP A 77 -71.32 -150.62 REMARK 500 SER A 78 87.65 2.38 REMARK 500 GLU A 79 119.31 101.14 REMARK 500 ILE A 124 -70.52 -58.90 REMARK 500 HIS A 126 -97.14 39.46 REMARK 500 THR A 134 -92.94 -95.54 REMARK 500 GLN A 200 24.72 -155.14 REMARK 500 SER A 241 -122.15 41.49 REMARK 500 ARG A 243 43.39 -164.40 REMARK 500 GLU A 306 -81.88 -127.27 REMARK 500 THR A 307 87.83 44.55 REMARK 500 PRO A 308 107.10 -46.53 REMARK 500 PRO A 366 108.67 -54.17 REMARK 500 ASP A 389 27.95 46.45 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 B12 A1415 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SO3 A1419 S REMARK 620 2 B12 A1415 N21 94.1 REMARK 620 3 B12 A1415 N22 87.1 89.5 REMARK 620 4 B12 A1415 N23 83.9 173.9 96.1 REMARK 620 5 B12 A1415 N24 87.0 84.3 171.1 89.9 REMARK 620 N 1 2 3 4 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B12 A1415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO3 A1419 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BB6 RELATED DB: PDB REMARK 900 STRUCTURE OF COBALAMIN-COMPLEXED BOVINE TRANSCOBALAMIN IN REMARK 900 MONOCLINIC CRYSTAL FORM REMARK 900 RELATED ID: 2BBC RELATED DB: PDB REMARK 900 STRUCTURE OF COBALAMIN-COMPLEXED BOVINE TRANSCOBALAMIN IN TRIGONAL REMARK 900 CRYSTAL FORM REMARK 900 RELATED ID: 2V3N RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC ANALYSIS OF UPPER AXIAL LIGAND SUBSTITUTIONS IN REMARK 900 COBALAMIN BOUND TO TRANSCOBALAMIN DBREF 2V3P A 1 414 UNP Q9XSC9 TCO2_BOVIN 19 432 SEQRES 1 A 414 ASN ILE CYS GLU ILE THR GLU VAL ASP SER THR LEU VAL SEQRES 2 A 414 GLU ARG LEU GLY GLN ARG LEU LEU PRO TRP MET ASP ARG SEQRES 3 A 414 LEU SER GLN GLU GLN LEU ASN PRO SER ILE TYR VAL GLY SEQRES 4 A 414 LEU ARG LEU SER SER LEU GLN ALA GLY ALA LYS GLU ALA SEQRES 5 A 414 HIS TYR LEU HIS SER LEU LYS LEU SER TYR GLN GLN SER SEQRES 6 A 414 LEU LEU ARG PRO ALA SER ASN LYS ASP ASP ASN ASP SER SEQRES 7 A 414 GLU ALA LYS PRO SER MET GLY GLN LEU ALA LEU TYR LEU SEQRES 8 A 414 LEU ALA LEU ARG ALA ASN CYS GLU PHE ILE GLY GLY ARG SEQRES 9 A 414 LYS GLY ASP ARG LEU VAL SER GLN LEU LYS ARG PHE LEU SEQRES 10 A 414 GLU ASP GLU LYS ARG ALA ILE GLY HIS ASN HIS GLN GLY SEQRES 11 A 414 HIS PRO ARG THR SER TYR TYR GLN TYR SER LEU GLY ILE SEQRES 12 A 414 LEU ALA LEU CYS VAL HIS GLN LYS ARG VAL HIS ASP SER SEQRES 13 A 414 VAL VAL GLY LYS LEU LEU TYR ALA VAL GLU HIS LYS PRO SEQRES 14 A 414 HIS LEU LEU GLN ASP HIS VAL SER VAL ASP THR MET ALA SEQRES 15 A 414 MET ALA GLY MET ALA PHE SER CYS LEU GLU LEU SER ASN SEQRES 16 A 414 LEU ASN PRO LYS GLN ARG ASN ARG ILE ASN LEU ALA LEU SEQRES 17 A 414 LYS ARG VAL GLN GLU LYS ILE LEU LYS ALA GLN THR PRO SEQRES 18 A 414 GLU GLY TYR PHE GLY ASN VAL TYR SER THR PRO LEU ALA SEQRES 19 A 414 LEU GLN LEU LEU MET GLY SER LEU ARG PRO SER VAL GLU SEQRES 20 A 414 LEU GLY THR ALA CYS LEU LYS ALA LYS ALA ALA LEU GLN SEQRES 21 A 414 ALA SER LEU GLN HIS LYS THR PHE GLN ASN PRO LEU MET SEQRES 22 A 414 ILE SER GLN LEU LEU PRO VAL LEU ASN GLN LYS SER TYR SEQRES 23 A 414 VAL ASP LEU ILE SER PRO ASP CYS GLN ALA PRO ARG ALA SEQRES 24 A 414 LEU LEU GLU PRO ALA LEU GLU THR PRO PRO GLN ALA LYS SEQRES 25 A 414 VAL PRO LYS PHE ILE ASP VAL LEU LEU LYS VAL SER GLY SEQRES 26 A 414 ILE SER PRO SER TYR ARG HIS SER VAL SER VAL PRO ALA SEQRES 27 A 414 GLY SER SER LEU GLU ASP ILE LEU LYS ASN ALA GLN GLU SEQRES 28 A 414 HIS GLY ARG PHE ARG PHE ARG THR GLN ALA SER LEU SER SEQRES 29 A 414 GLY PRO PHE LEU THR SER VAL LEU GLY ARG LYS ALA GLY SEQRES 30 A 414 GLU ARG GLU PHE TRP GLN VAL LEU ARG ASP PRO ASP THR SEQRES 31 A 414 PRO LEU GLN GLN GLY ILE ALA ASP TYR ARG PRO LYS ASP SEQRES 32 A 414 GLY GLU THR ILE GLU LEU ARG LEU VAL GLY TRP HET B12 A1415 91 HET CL A1416 1 HET CL A1417 1 HET CL A1418 1 HET SO3 A1419 4 HETNAM B12 COBALAMIN HETNAM CL CHLORIDE ION HETNAM SO3 SULFITE ION FORMUL 2 B12 C62 H89 CO N13 O14 P 2+ FORMUL 3 CL 3(CL 1-) FORMUL 6 SO3 O3 S 2- FORMUL 7 HOH *120(H2 O) HELIX 1 1 ASP A 9 ARG A 26 1 18 HELIX 2 2 ASN A 33 SER A 43 1 11 HELIX 3 3 ALA A 49 LEU A 67 1 19 HELIX 4 4 SER A 83 ASN A 97 1 15 HELIX 5 5 GLY A 102 GLY A 125 1 24 HELIX 6 6 SER A 135 VAL A 148 1 14 HELIX 7 7 VAL A 153 GLU A 166 1 14 HELIX 8 8 SER A 177 ASN A 195 1 19 HELIX 9 9 GLN A 200 ALA A 218 1 19 HELIX 10 10 SER A 230 MET A 239 1 10 HELIX 11 11 SER A 245 GLN A 264 1 20 HELIX 12 12 ASN A 270 ASN A 282 1 13 HELIX 13 13 SER A 285 SER A 291 5 7 HELIX 14 14 SER A 341 HIS A 352 1 12 SHEET 1 AA 5 TYR A 330 ALA A 338 0 SHEET 2 AA 5 LYS A 315 VAL A 323 -1 N VAL A 319 O VAL A 334 SHEET 3 AA 5 GLU A 405 GLY A 413 1 O ILE A 407 N LYS A 322 SHEET 4 AA 5 GLU A 380 ARG A 386 -1 N GLN A 383 O ARG A 410 SHEET 5 AA 5 THR A 390 LEU A 392 -1 O THR A 390 N ARG A 386 SHEET 1 AB 3 ARG A 356 SER A 362 0 SHEET 2 AB 3 GLY A 365 VAL A 371 -1 O PHE A 367 N GLN A 360 SHEET 3 AB 3 ARG A 374 ALA A 376 -1 O ARG A 374 N VAL A 371 SSBOND 1 CYS A 3 CYS A 252 1555 1555 2.05 SSBOND 2 CYS A 98 CYS A 294 1555 1555 2.08 SSBOND 3 CYS A 147 CYS A 190 1555 1555 2.06 LINK CO B12 A1415 S SO3 A1419 1555 1555 2.25 CISPEP 1 SER A 327 PRO A 328 0 1.69 CISPEP 2 ASP A 387 PRO A 388 0 13.88 SITE 1 AC1 35 GLY A 85 GLN A 86 THR A 134 TYR A 137 SITE 2 AC1 35 GLN A 138 ASP A 179 ASN A 227 TYR A 229 SITE 3 AC1 35 SER A 230 MET A 273 GLN A 276 SER A 362 SITE 4 AC1 35 LEU A 363 SER A 364 GLY A 365 PRO A 366 SITE 5 AC1 35 PHE A 367 LEU A 368 PHE A 381 TRP A 382 SITE 6 AC1 35 GLN A 383 VAL A 384 LEU A 392 GLN A 393 SITE 7 AC1 35 GLY A 395 TRP A 414 CL A1416 SO3 A1419 SITE 8 AC1 35 HOH A2056 HOH A2090 HOH A2116 HOH A2117 SITE 9 AC1 35 HOH A2118 HOH A2119 HOH A2120 SITE 1 AC2 6 TYR A 229 THR A 267 GLN A 269 ASN A 270 SITE 2 AC2 6 GLN A 394 B12 A1415 SITE 1 AC3 5 ARG A 356 PHE A 357 ARG A 358 SER A 370 SITE 2 AC3 5 GLY A 373 SITE 1 AC4 2 ARG A 108 GLN A 112 SITE 1 AC5 1 B12 A1415 CRYST1 100.390 100.390 129.742 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 0.009961 0.005751 0.000000 0.00000 SCALE2 0.000000 0.011502 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007708 0.00000