HEADER SIGNALING PROTEIN 10-MAR-15 5AMI TITLE CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN COMPLEX TITLE 2 WITH THALIDOMIDE, WASH I STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CEREBLON ISOFORM 4; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MAGNETOSPIRILLUM GRYPHISWALDENSE; SOURCE 3 ORGANISM_TAXID: 431944; SOURCE 4 STRAIN: MSR-1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SIGNALING PROTEIN, TERATOGENICITY, AROMATIC CAGE EXPDTA X-RAY DIFFRACTION AUTHOR M.D.HARTMANN,A.N.LUPAS,B.HERNANDEZ ALVAREZ REVDAT 2 10-JAN-24 5AMI 1 REMARK LINK REVDAT 1 01-JUL-15 5AMI 0 JRNL AUTH M.D.HARTMANN,I.BOICHENKO,M.COLES,A.N.LUPAS, JRNL AUTH 2 B.HERNANDEZ ALVAREZ JRNL TITL STRUCTURAL DYNAMICS OF THE CEREBLON LIGAND BINDING DOMAIN. JRNL REF PLOS ONE V. 10 28342 2015 JRNL REFN ESSN 1932-6203 JRNL PMID 26024445 JRNL DOI 10.1371/JOURNAL.PONE.0128342 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 29087 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1540 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2083 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.2870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2232 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 99 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.10000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -1.13000 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): 0.103 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.736 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2357 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2136 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3195 ; 2.235 ; 1.935 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4882 ; 1.155 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 287 ; 6.220 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 104 ;35.268 ;22.019 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 340 ;13.114 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;12.405 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 317 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2699 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 632 ; 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): 1154 ; 1.665 ; 1.665 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1153 ; 1.664 ; 1.665 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1433 ; 2.566 ; 2.483 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1203 ; 2.525 ; 1.948 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 3 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 20 A 151 REMARK 3 ORIGIN FOR THE GROUP (A): 19.7108 17.6589 1.6802 REMARK 3 T TENSOR REMARK 3 T11: 0.0054 T22: 0.1088 REMARK 3 T33: 0.0845 T12: 0.0095 REMARK 3 T13: -0.0112 T23: -0.0255 REMARK 3 L TENSOR REMARK 3 L11: 2.6009 L22: 1.8519 REMARK 3 L33: 4.5139 L12: 0.2670 REMARK 3 L13: 0.4242 L23: 1.0959 REMARK 3 S TENSOR REMARK 3 S11: -0.0553 S12: 0.0939 S13: -0.2021 REMARK 3 S21: -0.0048 S22: 0.0491 S23: 0.0373 REMARK 3 S31: -0.0363 S32: -0.0301 S33: 0.0061 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 : B 20 B 151 REMARK 3 ORIGIN FOR THE GROUP (A): 32.2557 8.2309 23.7781 REMARK 3 T TENSOR REMARK 3 T11: 0.0992 T22: 0.0755 REMARK 3 T33: 0.0684 T12: -0.0184 REMARK 3 T13: 0.0021 T23: 0.0148 REMARK 3 L TENSOR REMARK 3 L11: 2.4614 L22: 4.0460 REMARK 3 L33: 2.0624 L12: -1.8537 REMARK 3 L13: 0.1084 L23: -0.9025 REMARK 3 S TENSOR REMARK 3 S11: -0.0146 S12: -0.0619 S13: -0.1329 REMARK 3 S21: 0.2033 S22: -0.0192 S23: 0.0349 REMARK 3 S31: 0.0517 S32: 0.0485 S33: 0.0338 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 : C 16 C 150 REMARK 3 ORIGIN FOR THE GROUP (A): 30.6942 -4.6346 -4.1684 REMARK 3 T TENSOR REMARK 3 T11: 0.3274 T22: 0.3265 REMARK 3 T33: 0.3381 T12: -0.0940 REMARK 3 T13: 0.0585 T23: -0.0385 REMARK 3 L TENSOR REMARK 3 L11: 3.2703 L22: 4.9318 REMARK 3 L33: 3.5230 L12: -0.2889 REMARK 3 L13: 0.5445 L23: -0.7568 REMARK 3 S TENSOR REMARK 3 S11: 0.0127 S12: -0.0752 S13: -0.5061 REMARK 3 S21: -0.1995 S22: 0.0132 S23: 0.5974 REMARK 3 S31: 0.5577 S32: -0.5569 S33: -0.0259 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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. U VALUES WITH TLS ADDED. REMARK 4 REMARK 4 5AMI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1290063292. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30628 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 37.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.230 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.23 REMARK 200 R MERGE FOR SHELL (I) : 0.68000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 4V2Y REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE PH 4.6, 20 REMARK 280 %(W/V) PEG 6000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 28.62500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.36400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.82800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.36400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.62500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.82800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 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: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 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: C 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 ALA A 0 REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 LEU A 3 REMARK 465 ASP A 4 REMARK 465 ALA A 5 REMARK 465 GLY A 6 REMARK 465 GLY A 7 REMARK 465 GLN A 8 REMARK 465 ASN A 9 REMARK 465 SER A 10 REMARK 465 THR A 11 REMARK 465 GLN A 12 REMARK 465 MET A 13 REMARK 465 VAL A 14 REMARK 465 LEU A 15 REMARK 465 ALA A 16 REMARK 465 PRO A 17 REMARK 465 GLY A 18 REMARK 465 ALA A 19 REMARK 465 ASP A 124 REMARK 465 ALA B 0 REMARK 465 MET B 1 REMARK 465 PRO B 2 REMARK 465 LEU B 3 REMARK 465 ASP B 4 REMARK 465 ALA B 5 REMARK 465 GLY B 6 REMARK 465 GLY B 7 REMARK 465 GLN B 8 REMARK 465 ASN B 9 REMARK 465 SER B 10 REMARK 465 THR B 11 REMARK 465 GLN B 12 REMARK 465 MET B 13 REMARK 465 VAL B 14 REMARK 465 LEU B 15 REMARK 465 ALA B 16 REMARK 465 PRO B 17 REMARK 465 GLY B 18 REMARK 465 ALA B 19 REMARK 465 ASP B 124 REMARK 465 ALA C 0 REMARK 465 MET C 1 REMARK 465 PRO C 2 REMARK 465 LEU C 3 REMARK 465 ASP C 4 REMARK 465 ALA C 5 REMARK 465 GLY C 6 REMARK 465 GLY C 7 REMARK 465 GLN C 8 REMARK 465 ASN C 9 REMARK 465 SER C 10 REMARK 465 THR C 11 REMARK 465 GLN C 12 REMARK 465 MET C 13 REMARK 465 VAL C 14 REMARK 465 LEU C 15 REMARK 465 PRO C 39 REMARK 465 MET C 40 REMARK 465 GLY C 41 REMARK 465 GLY C 42 REMARK 465 ASP C 43 REMARK 465 HIS C 44 REMARK 465 GLU C 45 REMARK 465 GLY C 71 REMARK 465 ALA C 72 REMARK 465 PRO C 73 REMARK 465 SER C 74 REMARK 465 GLY C 75 REMARK 465 GLU C 76 REMARK 465 PHE C 77 REMARK 465 SER C 78 REMARK 465 TRP C 79 REMARK 465 PHE C 80 REMARK 465 LYS C 81 REMARK 465 GLY C 82 REMARK 465 TYR C 83 REMARK 465 ASP C 84 REMARK 465 GLY C 103 REMARK 465 GLY C 104 REMARK 465 SER C 105 REMARK 465 GLN C 106 REMARK 465 PRO C 107 REMARK 465 GLN C 108 REMARK 465 ASP C 124 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 ARG B 68 CD NE CZ NH1 NH2 REMARK 470 GLU B 76 CG CD OE1 OE2 REMARK 470 GLN B 106 CG CD OE1 NE2 REMARK 470 ARG C 34 CG CD NE CZ NH1 NH2 REMARK 470 HIS C 46 CG ND1 CD2 CE1 NE2 REMARK 470 ARG C 57 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 68 CG CD NE CZ NH1 NH2 REMARK 470 TRP C 85 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP C 85 CZ3 CH2 REMARK 470 TYR C 101 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU C 102 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 2024 O HOH C 2007 4455 2.09 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 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 3.1 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 CYS A 27 -11.19 -143.97 REMARK 500 ILE A 31 -56.04 -122.66 REMARK 500 ILE C 31 -50.47 -123.63 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 ZN A 150 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 24 SG REMARK 620 2 CYS A 27 SG 113.7 REMARK 620 3 CYS A 90 SG 108.9 102.1 REMARK 620 4 CYS A 93 SG 108.4 111.7 112.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 150 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 24 SG REMARK 620 2 CYS B 27 SG 112.8 REMARK 620 3 CYS B 90 SG 110.3 106.0 REMARK 620 4 CYS B 93 SG 104.0 113.2 110.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 150 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 24 SG REMARK 620 2 CYS C 27 SG 114.2 REMARK 620 3 CYS C 90 SG 108.0 101.4 REMARK 620 4 CYS C 93 SG 106.8 112.3 114.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EF2 A 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EF2 B 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 150 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AMH RELATED DB: PDB REMARK 900 CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN COMPLEX REMARK 900 WITH THALIDOMIDE, TRIGONAL CRYSTAL FORM REMARK 900 RELATED ID: 5AMJ RELATED DB: PDB REMARK 900 CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN COMPLEX REMARK 900 WITH THALIDOMIDE, WASH II STRUCTURE REMARK 900 RELATED ID: 5AMK RELATED DB: PDB REMARK 900 CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN REMARK 900 MULTIPLE CONFORMATIONS, HEXAGONAL CRYSTAL FORM DBREF 5AMI A 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 DBREF 5AMI B 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 DBREF 5AMI C 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 SEQADV 5AMI ALA A 0 UNP A4TVL0 EXPRESSION TAG SEQADV 5AMI ALA B 0 UNP A4TVL0 EXPRESSION TAG SEQADV 5AMI ALA C 0 UNP A4TVL0 EXPRESSION TAG SEQRES 1 A 125 ALA MET PRO LEU ASP ALA GLY GLY GLN ASN SER THR GLN SEQRES 2 A 125 MET VAL LEU ALA PRO GLY ALA SER ILE PHE ARG CYS ARG SEQRES 3 A 125 GLN CYS GLY GLN THR ILE SER ARG ARG ASP TRP LEU LEU SEQRES 4 A 125 PRO MET GLY GLY ASP HIS GLU HIS VAL VAL PHE ASN PRO SEQRES 5 A 125 ALA GLY MET ILE PHE ARG VAL TRP CYS PHE SER LEU ALA SEQRES 6 A 125 GLN GLY LEU ARG LEU ILE GLY ALA PRO SER GLY GLU PHE SEQRES 7 A 125 SER TRP PHE LYS GLY TYR ASP TRP THR ILE ALA LEU CYS SEQRES 8 A 125 GLY GLN CYS GLY SER HIS LEU GLY TRP HIS TYR GLU GLY SEQRES 9 A 125 GLY SER GLN PRO GLN THR PHE PHE GLY LEU ILE LYS ASP SEQRES 10 A 125 ARG LEU ALA GLU GLY PRO ALA ASP SEQRES 1 B 125 ALA MET PRO LEU ASP ALA GLY GLY GLN ASN SER THR GLN SEQRES 2 B 125 MET VAL LEU ALA PRO GLY ALA SER ILE PHE ARG CYS ARG SEQRES 3 B 125 GLN CYS GLY GLN THR ILE SER ARG ARG ASP TRP LEU LEU SEQRES 4 B 125 PRO MET GLY GLY ASP HIS GLU HIS VAL VAL PHE ASN PRO SEQRES 5 B 125 ALA GLY MET ILE PHE ARG VAL TRP CYS PHE SER LEU ALA SEQRES 6 B 125 GLN GLY LEU ARG LEU ILE GLY ALA PRO SER GLY GLU PHE SEQRES 7 B 125 SER TRP PHE LYS GLY TYR ASP TRP THR ILE ALA LEU CYS SEQRES 8 B 125 GLY GLN CYS GLY SER HIS LEU GLY TRP HIS TYR GLU GLY SEQRES 9 B 125 GLY SER GLN PRO GLN THR PHE PHE GLY LEU ILE LYS ASP SEQRES 10 B 125 ARG LEU ALA GLU GLY PRO ALA ASP SEQRES 1 C 125 ALA MET PRO LEU ASP ALA GLY GLY GLN ASN SER THR GLN SEQRES 2 C 125 MET VAL LEU ALA PRO GLY ALA SER ILE PHE ARG CYS ARG SEQRES 3 C 125 GLN CYS GLY GLN THR ILE SER ARG ARG ASP TRP LEU LEU SEQRES 4 C 125 PRO MET GLY GLY ASP HIS GLU HIS VAL VAL PHE ASN PRO SEQRES 5 C 125 ALA GLY MET ILE PHE ARG VAL TRP CYS PHE SER LEU ALA SEQRES 6 C 125 GLN GLY LEU ARG LEU ILE GLY ALA PRO SER GLY GLU PHE SEQRES 7 C 125 SER TRP PHE LYS GLY TYR ASP TRP THR ILE ALA LEU CYS SEQRES 8 C 125 GLY GLN CYS GLY SER HIS LEU GLY TRP HIS TYR GLU GLY SEQRES 9 C 125 GLY SER GLN PRO GLN THR PHE PHE GLY LEU ILE LYS ASP SEQRES 10 C 125 ARG LEU ALA GLU GLY PRO ALA ASP HET ZN A 150 1 HET EF2 A 151 19 HET ZN B 150 1 HET EF2 B 151 19 HET ZN C 150 1 HETNAM ZN ZINC ION HETNAM EF2 S-THALIDOMIDE FORMUL 4 ZN 3(ZN 2+) FORMUL 5 EF2 2(C13 H10 N2 O4) FORMUL 9 HOH *99(H2 O) HELIX 1 1 ASP A 35 LEU A 37 5 3 HELIX 2 2 ASP B 35 LEU B 37 5 3 HELIX 3 3 PRO B 39 ASP B 43 5 5 HELIX 4 4 ASP C 35 LEU C 37 5 3 SHEET 1 AA 3 THR A 30 ARG A 33 0 SHEET 2 AA 3 ILE A 21 CYS A 24 -1 O PHE A 22 N ILE A 31 SHEET 3 AA 3 LEU A 118 GLY A 121 -1 O ALA A 119 N ARG A 23 SHEET 1 AB 6 GLU A 45 PHE A 49 0 SHEET 2 AB 6 ILE A 55 PHE A 61 -1 O PHE A 56 N VAL A 48 SHEET 3 AB 6 PHE A 110 ILE A 114 -1 O PHE A 111 N PHE A 61 SHEET 4 AB 6 HIS A 96 GLU A 102 -1 O LEU A 97 N ILE A 114 SHEET 5 AB 6 ASP A 84 CYS A 90 -1 O ASP A 84 N GLU A 102 SHEET 6 AB 6 LEU A 67 SER A 74 -1 O ARG A 68 N LEU A 89 SHEET 1 BA 3 THR B 30 ARG B 33 0 SHEET 2 BA 3 ILE B 21 CYS B 24 -1 O PHE B 22 N ILE B 31 SHEET 3 BA 3 LEU B 118 GLY B 121 -1 O ALA B 119 N ARG B 23 SHEET 1 BB 6 GLU B 45 PHE B 49 0 SHEET 2 BB 6 ILE B 55 PHE B 61 -1 O PHE B 56 N VAL B 48 SHEET 3 BB 6 THR B 109 ILE B 114 -1 O PHE B 111 N PHE B 61 SHEET 4 BB 6 HIS B 96 GLY B 103 -1 O LEU B 97 N ILE B 114 SHEET 5 BB 6 TYR B 83 CYS B 90 -1 O ASP B 84 N GLU B 102 SHEET 6 BB 6 LEU B 67 SER B 74 -1 O ARG B 68 N LEU B 89 SHEET 1 CA 3 THR C 30 ARG C 33 0 SHEET 2 CA 3 ILE C 21 CYS C 24 -1 O PHE C 22 N ILE C 31 SHEET 3 CA 3 LEU C 118 GLY C 121 -1 O ALA C 119 N ARG C 23 SHEET 1 CB 6 VAL C 47 PHE C 49 0 SHEET 2 CB 6 ILE C 55 PHE C 61 -1 O PHE C 56 N VAL C 48 SHEET 3 CB 6 PHE C 110 ILE C 114 -1 O PHE C 111 N PHE C 61 SHEET 4 CB 6 HIS C 96 TYR C 101 -1 O LEU C 97 N ILE C 114 SHEET 5 CB 6 THR C 86 CYS C 90 -1 O THR C 86 N HIS C 100 SHEET 6 CB 6 LEU C 67 ILE C 70 -1 O ARG C 68 N LEU C 89 LINK SG CYS A 24 ZN ZN A 150 1555 1555 2.32 LINK SG CYS A 27 ZN ZN A 150 1555 1555 2.36 LINK SG CYS A 90 ZN ZN A 150 1555 1555 2.29 LINK SG CYS A 93 ZN ZN A 150 1555 1555 2.34 LINK SG CYS B 24 ZN ZN B 150 1555 1555 2.41 LINK SG CYS B 27 ZN ZN B 150 1555 1555 2.25 LINK SG CYS B 90 ZN ZN B 150 1555 1555 2.34 LINK SG CYS B 93 ZN ZN B 150 1555 1555 2.33 LINK SG CYS C 24 ZN ZN C 150 1555 1555 2.37 LINK SG CYS C 27 ZN ZN C 150 1555 1555 2.33 LINK SG CYS C 90 ZN ZN C 150 1555 1555 2.34 LINK SG CYS C 93 ZN ZN C 150 1555 1555 2.38 CISPEP 1 GLN A 106 PRO A 107 0 6.72 CISPEP 2 GLN B 106 PRO B 107 0 -5.71 SITE 1 AC1 4 CYS A 24 CYS A 27 CYS A 90 CYS A 93 SITE 1 AC2 9 ASN A 50 PRO A 51 GLU A 76 PHE A 77 SITE 2 AC2 9 SER A 78 TRP A 79 TRP A 85 TRP A 99 SITE 3 AC2 9 TYR A 101 SITE 1 AC3 4 CYS B 24 CYS B 27 CYS B 90 CYS B 93 SITE 1 AC4 10 ASN B 50 PRO B 51 PHE B 77 SER B 78 SITE 2 AC4 10 TRP B 79 TRP B 85 TRP B 99 TYR B 101 SITE 3 AC4 10 PRO C 51 ALA C 52 SITE 1 AC5 4 CYS C 24 CYS C 27 CYS C 90 CYS C 93 CRYST1 57.250 59.656 86.728 90.00 90.00 90.00 P 21 21 21 12 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 0.017467 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016763 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011530 0.00000