PDB Short entry for 3IHO HEADER HYDROLASE 30-JUL-09 3IHO TITLE THE C-TERMINAL GLYCOSYLASE DOMAIN OF HUMAN MBD4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL GLYCOSYLASE DOMAIN; COMPND 5 SYNONYM: METHYL-CPG-BINDING PROTEIN MBD4, METHYL-CPG-BINDING COMPND 6 ENDONUCLEASE 1, MISMATCH-SPECIFIC DNA N-GLYCOSYLASE; COMPND 7 EC: 3.2.2.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MBD4, MED1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MBD4, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, DNA KEYWDS 2 DAMAGE, DNA REPAIR, DNA-BINDING, HYDROLASE, NUCLEUS EXPDTA X-RAY DIFFRACTION AUTHOR M.F.AMAYA,C.XU,C.B.BIAN,C.BOUNTRA,J.WEIGELT,C.H.ARROWSMITH, AUTHOR 2 A.M.EDWARDS,A.BOCHKAREV,J.MIN,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 21-FEB-24 3IHO 1 REMARK REVDAT 3 01-NOV-17 3IHO 1 REMARK REVDAT 2 13-JUL-11 3IHO 1 VERSN REVDAT 1 25-AUG-09 3IHO 0 JRNL AUTH C.XU,C.B.BIAN,M.F.AMAYA,C.BOUNTRA,J.WEIGELT,C.H.ARROWSMITH, JRNL AUTH 2 A.M.EDWARDS,A.BOCHKAREV,J.MIN JRNL TITL THE C-TERMINAL GLYCOSYLASE DOMAIN OF HUMAN MBD4 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 4589 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 218 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 207 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 57.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.1640 REMARK 3 BIN FREE R VALUE SET COUNT : 11 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1146 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 12 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) : 24.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.89000 REMARK 3 B22 (A**2) : 1.89000 REMARK 3 B33 (A**2) : -2.83000 REMARK 3 B12 (A**2) : 0.94000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.412 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.286 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 22.469 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.872 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1189 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1626 ; 1.978 ; 1.923 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 137 ; 6.489 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 57 ;32.271 ;23.509 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 183 ;18.877 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;18.907 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 168 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 923 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 693 ; 0.804 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1119 ; 1.610 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 496 ; 2.544 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 507 ; 4.228 ; 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 : 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 411 A 422 REMARK 3 ORIGIN FOR THE GROUP (A): 29.6082 -2.2984 18.8875 REMARK 3 T TENSOR REMARK 3 T11: 0.2552 T22: 0.2242 REMARK 3 T33: 0.2384 T12: -0.0088 REMARK 3 T13: -0.0256 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 2.3869 L22: 0.9038 REMARK 3 L33: 0.1996 L12: -1.2729 REMARK 3 L13: -0.5752 L23: 0.2700 REMARK 3 S TENSOR REMARK 3 S11: -0.1071 S12: -0.2526 S13: 0.2484 REMARK 3 S21: 0.2138 S22: 0.1043 S23: -0.2419 REMARK 3 S31: -0.0405 S32: 0.0850 S33: 0.0028 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 423 A 528 REMARK 3 ORIGIN FOR THE GROUP (A): 18.5195 -16.7398 19.0520 REMARK 3 T TENSOR REMARK 3 T11: 0.0959 T22: 0.1004 REMARK 3 T33: 0.0322 T12: 0.0210 REMARK 3 T13: -0.0096 T23: -0.0295 REMARK 3 L TENSOR REMARK 3 L11: 1.9079 L22: 2.2423 REMARK 3 L33: 3.3853 L12: 1.5615 REMARK 3 L13: -1.8056 L23: -0.4997 REMARK 3 S TENSOR REMARK 3 S11: -0.0240 S12: 0.1431 S13: 0.0100 REMARK 3 S21: 0.0691 S22: 0.1043 S23: 0.0492 REMARK 3 S31: 0.0285 S32: -0.1239 S33: -0.0802 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 529 A 548 REMARK 3 ORIGIN FOR THE GROUP (A): 27.5193 -1.4030 8.0913 REMARK 3 T TENSOR REMARK 3 T11: 0.6046 T22: 0.2538 REMARK 3 T33: 0.0440 T12: -0.2387 REMARK 3 T13: -0.1173 T23: 0.0566 REMARK 3 L TENSOR REMARK 3 L11: 1.3656 L22: 4.5049 REMARK 3 L33: 7.1687 L12: 2.1441 REMARK 3 L13: 1.9521 L23: 0.8853 REMARK 3 S TENSOR REMARK 3 S11: -0.6490 S12: 0.3560 S13: 0.2393 REMARK 3 S21: -0.4816 S22: 0.3227 S23: 0.3758 REMARK 3 S31: -1.8203 S32: 0.7992 S33: 0.3263 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 REMARK 4 REMARK 4 3IHO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054423. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5287 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.697 REMARK 200 RESOLUTION RANGE LOW (A) : 51.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.31500 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.2M LI SULFATE, 0.1M REMARK 280 HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.77050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.11621 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.65200 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 41.77050 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 24.11621 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 24.65200 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 41.77050 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 24.11621 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 24.65200 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.23242 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 49.30400 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 48.23242 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 49.30400 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 48.23242 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 49.30400 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 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 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 A 468 CG CD NE CZ NH1 NH2 REMARK 470 SER A 470 OG REMARK 470 LYS A 472 CG CD CE NZ REMARK 470 LYS A 480 CG CD CE NZ REMARK 470 LEU A 508 CG CD1 CD2 REMARK 470 LEU A 511 CG CD1 CD2 REMARK 470 GLN A 527 CG CD OE1 NE2 REMARK 470 LYS A 529 CG CD CE NZ REMARK 470 LYS A 562 CG CD CE NZ 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 LEU A 524 CB - CG - CD1 ANGL. DEV. = -10.4 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 PRO A 444 -1.67 -57.97 REMARK 500 ARG A 468 51.89 36.10 REMARK 500 GLU A 552 32.56 -146.06 REMARK 500 GLU A 559 51.41 -144.56 REMARK 500 REMARK 500 REMARK: NULL DBREF 3IHO A 437 574 UNP O95243 MBD4_HUMAN 437 574 SEQRES 1 A 138 LYS TRP THR PRO PRO ARG SER PRO PHE ASN LEU VAL GLN SEQRES 2 A 138 GLU THR LEU PHE HIS ASP PRO TRP LYS LEU LEU ILE ALA SEQRES 3 A 138 THR ILE PHE LEU ASN ARG THR SER GLY LYS MET ALA ILE SEQRES 4 A 138 PRO VAL LEU TRP LYS PHE LEU GLU LYS TYR PRO SER ALA SEQRES 5 A 138 GLU VAL ALA ARG THR ALA ASP TRP ARG ASP VAL SER GLU SEQRES 6 A 138 LEU LEU LYS PRO LEU GLY LEU TYR ASP LEU ARG ALA LYS SEQRES 7 A 138 THR ILE VAL LYS PHE SER ASP GLU TYR LEU THR LYS GLN SEQRES 8 A 138 TRP LYS TYR PRO ILE GLU LEU HIS GLY ILE GLY LYS TYR SEQRES 9 A 138 GLY ASN ASP SER TYR ARG ILE PHE CYS VAL ASN GLU TRP SEQRES 10 A 138 LYS GLN VAL HIS PRO GLU ASP HIS LYS LEU ASN LYS TYR SEQRES 11 A 138 HIS ASP TRP LEU TRP GLU ASN HIS FORMUL 2 HOH *12(H2 O) HELIX 1 1 VAL A 448 PHE A 453 1 6 HELIX 2 2 ASP A 455 ASN A 467 1 13 HELIX 3 3 SER A 470 TYR A 485 1 16 HELIX 4 4 SER A 487 ARG A 492 1 6 HELIX 5 5 ASP A 495 LYS A 504 1 10 HELIX 6 6 LEU A 508 LYS A 526 1 19 HELIX 7 7 TYR A 530 LEU A 534 5 5 HELIX 8 8 GLY A 538 CYS A 549 1 12 HELIX 9 9 ASP A 560 HIS A 574 1 15 CISPEP 1 LYS A 504 PRO A 505 0 -2.99 CRYST1 83.541 83.541 73.956 90.00 90.00 120.00 H 3 9 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 0.011970 0.006911 0.000000 0.00000 SCALE2 0.000000 0.013822 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013522 0.00000