HEADER SIGNALING PROTEIN 15-OCT-14 4V2Y TITLE CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN TITLE 2 COMPLEX WITH THALIDOMIDE 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 1 17-DEC-14 4V2Y 0 JRNL AUTH M.D.HARTMANN,I.BOICHENKO,M.COLES,F.ZANINI,A.N.LUPAS, JRNL AUTH 2 B.HERNANDEZ ALVAREZ JRNL TITL THALIDOMIDE MIMICS URIDINE BINDING TO AN AROMATIC CAGE IN JRNL TITL 2 CEREBLON. JRNL REF J.STRUCT.BIOL. V. 188 225 2014 JRNL REFN ISSN 1047-8477 JRNL PMID 25448889 JRNL DOI 10.1016/J.JSB.2014.10.010 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU, REMARK 3 STEINER,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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.71 REMARK 3 NUMBER OF REFLECTIONS : 57028 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) : 0.16363 REMARK 3 R VALUE (WORKING SET) : 0.16201 REMARK 3 FREE R VALUE : 0.19457 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 3003 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) : 1.398 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.434 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4012 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.319 REMARK 3 BIN FREE R VALUE SET COUNT : 213 REMARK 3 BIN FREE R VALUE : 0.335 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2506 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 215 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.788 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.20 REMARK 3 B22 (A**2) : 0.48 REMARK 3 B33 (A**2) : -0.68 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.057 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.061 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.929 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2666 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2398 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3638 ; 2.298 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5500 ; 0.933 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 335 ; 6.643 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;37.266 ;21.901 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 390 ;12.486 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;15.251 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 352 ; 0.134 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3094 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 725 ; 0.002 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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 19 A 123 REMARK 3 ORIGIN FOR THE GROUP (A): 19.2827 17.9308 2.1330 REMARK 3 T TENSOR REMARK 3 T11: 0.0075 T22: 0.0653 REMARK 3 T33: 0.0700 T12: 0.0085 REMARK 3 T13: -0.0074 T23: -0.0254 REMARK 3 L TENSOR REMARK 3 L11: 1.4457 L22: 1.2501 REMARK 3 L33: 3.4412 L12: 0.1344 REMARK 3 L13: 0.8988 L23: 0.8793 REMARK 3 S TENSOR REMARK 3 S11: 0.0585 S12: 0.0499 S13: -0.1502 REMARK 3 S21: 0.0097 S22: -0.0043 S23: 0.0517 REMARK 3 S31: 0.1377 S32: -0.0057 S33: -0.0543 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 123 REMARK 3 ORIGIN FOR THE GROUP (A): 31.7325 7.7089 24.0094 REMARK 3 T TENSOR REMARK 3 T11: 0.0292 T22: 0.0526 REMARK 3 T33: 0.0566 T12: -0.0117 REMARK 3 T13: 0.0106 T23: 0.0130 REMARK 3 L TENSOR REMARK 3 L11: 1.8702 L22: 1.8085 REMARK 3 L33: 1.5334 L12: -0.8053 REMARK 3 L13: 0.3240 L23: -0.4224 REMARK 3 S TENSOR REMARK 3 S11: -0.0055 S12: -0.0069 S13: -0.1411 REMARK 3 S21: 0.0240 S22: -0.0006 S23: 0.1189 REMARK 3 S31: 0.0267 S32: -0.0251 S33: 0.0061 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 19 C 123 REMARK 3 ORIGIN FOR THE GROUP (A): 27.7900 -6.5007 -6.8950 REMARK 3 T TENSOR REMARK 3 T11: 0.0869 T22: 0.1352 REMARK 3 T33: 0.1204 T12: -0.0107 REMARK 3 T13: 0.0087 T23: -0.0061 REMARK 3 L TENSOR REMARK 3 L11: 2.6797 L22: 3.0098 REMARK 3 L33: 2.5063 L12: 1.3954 REMARK 3 L13: 0.3100 L23: 0.0378 REMARK 3 S TENSOR REMARK 3 S11: 0.0219 S12: 0.0127 S13: -0.1005 REMARK 3 S21: -0.1272 S22: 0.0136 S23: 0.2755 REMARK 3 S31: 0.1874 S32: -0.3183 S33: -0.0355 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 REMARK 3 RIDING POSITIONS. REMARK 3 U VALUES WITH TLS ADDED REMARK 4 REMARK 4 4V2Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-OCT-14. REMARK 100 THE PDBE ID CODE IS EBI-61990. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-11 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 (PILATUS 6M) REMARK 200 DETECTOR MANUFACTURER : DECTRIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60181 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.40 REMARK 200 RESOLUTION RANGE LOW (A) : 37.30 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.69 REMARK 200 R MERGE (I) : 0.07 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.46 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.39 REMARK 200 R MERGE FOR SHELL (I) : 0.73 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.73 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.8 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MAGNESIUM CHLORIDE, 0.1 M REMARK 280 SODIUM CITRATE PH 5, 15%(W/V) PEG 4000 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 28.24500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.23500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.02000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.23500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.24500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.02000 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 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 ALA C 16 REMARK 465 PRO C 17 REMARK 465 GLY C 41 REMARK 465 GLY C 42 REMARK 465 ASP C 43 REMARK 465 HIS C 44 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 LYS A 81 CE NZ REMARK 470 ARG B 33 NE CZ NH1 NH2 REMARK 470 ARG C 33 NE CZ NH1 NH2 REMARK 470 MET C 54 CG SD CE REMARK 470 GLU C 76 CG CD OE1 OE2 REMARK 470 LYS C 81 CG CD CE NZ REMARK 470 GLN C 106 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NE2B GLN A 29 O HOH A 2016 1.92 REMARK 500 NH1B ARG A 68 O HOH A 2048 2.12 REMARK 500 NH2B ARG A 68 O HOH A 2048 2.11 REMARK 500 NE A ARG A 117 O HOH A 2079 2.16 REMARK 500 NE A ARG A 117 O HOH A 2095 2.11 REMARK 500 CZ A ARG A 117 O HOH A 2079 1.44 REMARK 500 CZ A ARG A 117 O HOH A 2095 1.84 REMARK 500 NH1A ARG A 117 O HOH A 2079 0.96 REMARK 500 NH2A ARG A 117 O HOH A 2095 1.22 REMARK 500 NE B ARG A 117 O HOH A 2011 1.88 REMARK 500 CZ B ARG A 117 O HOH A 2011 1.08 REMARK 500 CZ B ARG A 117 O HOH A 2010 1.74 REMARK 500 NH1B ARG A 117 O HOH A 2011 0.48 REMARK 500 NH2B ARG A 117 O HOH A 2010 0.56 REMARK 500 REMARK 500 REMARK: NULL 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 121 N GLY A 121 CA -0.095 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 23 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 23 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 34 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP B 43 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG C 23 NE - CZ - NH2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG C 25 NE - CZ - NH1 ANGL. DEV. = 3.2 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 SER A 20 -31.61 -134.85 REMARK 500 CYS A 27 -22.38 -142.27 REMARK 500 ILE A 31 -52.66 -122.19 REMARK 500 GLN B 106 71.66 43.08 REMARK 500 ILE C 31 -52.06 -120.12 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 90 SG REMARK 620 2 CYS A 27 SG 100.6 REMARK 620 3 CYS A 24 SG 108.5 113.9 REMARK 620 4 CYS A 93 SG 112.1 111.9 109.5 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 90 SG REMARK 620 2 CYS B 24 SG 110.9 REMARK 620 3 CYS B 27 SG 103.5 114.3 REMARK 620 4 CYS B 93 SG 111.8 103.0 113.5 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 114.0 REMARK 620 3 CYS C 90 SG 108.8 101.7 REMARK 620 4 CYS C 93 SG 107.6 111.2 113.5 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 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EF2 C 151 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4V2Z RELATED DB: PDB REMARK 900 CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE REMARK 900 IN COMPLEX WITH POMALIDOMIDE REMARK 900 RELATED ID: 4V30 RELATED DB: PDB REMARK 900 CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE REMARK 900 IN COMPLEX WITH LENALIDOMIDE REMARK 900 RELATED ID: 4V31 RELATED DB: PDB REMARK 900 CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE REMARK 900 IN COMPLEX WITH DEOXYURIDINE REMARK 900 RELATED ID: 4V32 RELATED DB: PDB REMARK 900 CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE REMARK 900 IN COMPLEX WITH THALIDOMIDE, Y101F MUTANT DBREF 4V2Y A 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 DBREF 4V2Y B 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 DBREF 4V2Y C 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 SEQADV 4V2Y ALA A 0 UNP A4TVL0 EXPRESSION TAG SEQADV 4V2Y ALA B 0 UNP A4TVL0 EXPRESSION TAG SEQADV 4V2Y 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 HET EF2 C 151 19 HETNAM EF2 S-THALIDOMIDE HETNAM ZN ZINC ION FORMUL 4 EF2 3(C13 H10 N2 O4) FORMUL 5 ZN 3(ZN 2+) FORMUL 6 HOH *215(H2 O) HELIX 1 1 PRO B 39 ASP B 43 5 5 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 GLU B 102 -1 O LEU B 97 N ILE B 114 SHEET 5 BB 6 ASP B 84 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 HIS C 46 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 THR C 109 ILE C 114 -1 O PHE C 111 N PHE C 61 SHEET 4 CB 6 HIS C 96 GLU C 102 -1 O LEU C 97 N ILE C 114 SHEET 5 CB 6 ASP C 84 CYS C 90 -1 O ASP C 84 N GLU C 102 SHEET 6 CB 6 LEU C 67 SER C 74 -1 O ARG C 68 N LEU C 89 LINK ZN ZN A 150 SG CYS A 90 1555 1555 2.37 LINK ZN ZN A 150 SG CYS A 27 1555 1555 2.32 LINK ZN ZN A 150 SG CYS A 24 1555 1555 2.34 LINK ZN ZN A 150 SG CYS A 93 1555 1555 2.31 LINK ZN ZN B 150 SG CYS B 90 1555 1555 2.33 LINK ZN ZN B 150 SG CYS B 24 1555 1555 2.35 LINK ZN ZN B 150 SG CYS B 27 1555 1555 2.34 LINK ZN ZN B 150 SG CYS B 93 1555 1555 2.36 LINK ZN ZN C 150 SG CYS C 27 1555 1555 2.30 LINK ZN ZN C 150 SG CYS C 90 1555 1555 2.37 LINK ZN ZN C 150 SG CYS C 93 1555 1555 2.29 LINK ZN ZN C 150 SG CYS C 24 1555 1555 2.30 CISPEP 1 GLN A 106 PRO A 107 0 6.27 CISPEP 2 GLN B 106 PRO B 107 0 -2.36 CISPEP 3 GLN C 106 PRO C 107 0 -0.15 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 PHE A 77 SER A 78 SITE 2 AC2 9 TRP A 79 TRP A 85 TRP A 99 TYR A 101 SITE 3 AC2 9 HOH A2098 SITE 1 AC3 4 CYS B 24 CYS B 27 CYS B 90 CYS B 93 SITE 1 AC4 8 ASN B 50 PRO B 51 PHE B 77 SER B 78 SITE 2 AC4 8 TRP B 79 TRP B 85 TRP B 99 TYR B 101 SITE 1 AC5 4 CYS C 24 CYS C 27 CYS C 90 CYS C 93 SITE 1 AC6 11 ILE B 70 ASN C 50 PRO C 51 PHE C 56 SITE 2 AC6 11 PHE C 77 SER C 78 TRP C 79 TRP C 85 SITE 3 AC6 11 TRP C 99 TYR C 101 HOH C2045 CRYST1 56.490 60.040 88.470 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 0.017702 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016656 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011303 0.00000