HEADER TRANSFERASE 08-MAY-14 4QBR TITLE CRYSTAL STRUCTURE OF DNMT3A ADD DOMAIN G550D MUTANT BOUND TO H3 TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 3A; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: ADD DOMAIN, UNP RESIDUES 476-611; COMPND 5 SYNONYM: DNMT3A, DNA METHYLTRANSFERASE HSAIIIA, DNA MTASE HSAIIIA, COMPND 6 M.HSAIIIA; COMPND 7 EC: 2.1.1.37; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: HISTONE H3; COMPND 12 CHAIN: P, E; COMPND 13 FRAGMENT: H3 N-TERMINAL; COMPND 14 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: DNMT3A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS ZINC FINGER, HISTONE BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,H.LI REVDAT 2 20-MAR-24 4QBR 1 REMARK SEQADV LINK REVDAT 1 13-MAY-15 4QBR 0 JRNL AUTH K.NOH,H.WANG,H.KIM,W.WENDERSKI,F.FANG,C.LI,S.DEWELL,X.WU, JRNL AUTH 2 A.FERRIS,S.H.HUGHES,D.ZHENG,A.M.MELNICK,D.J.PATEL,H.LI, JRNL AUTH 3 C.D.ALLIS JRNL TITL ENGINEERING OF A HISTONE-RECOGNITION DOMAIN IN A DE NOVO DNA JRNL TITL 2 METHYLTRANSFERASE ALTERS THE EPIGENETIC LANDSCAPE OF ESCS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 19072 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 979 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 36.1421 - 3.6368 0.97 2599 135 0.1719 0.1969 REMARK 3 2 3.6368 - 2.8870 0.97 2624 139 0.1748 0.2146 REMARK 3 3 2.8870 - 2.5222 0.97 2589 146 0.1896 0.2395 REMARK 3 4 2.5222 - 2.2916 0.97 2595 147 0.1735 0.2408 REMARK 3 5 2.2916 - 2.1274 0.96 2601 127 0.1714 0.2526 REMARK 3 6 2.1274 - 2.0020 0.96 2541 144 0.1836 0.2342 REMARK 3 7 2.0020 - 1.9017 0.95 2544 141 0.2052 0.2895 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 2308 REMARK 3 ANGLE : 1.093 3112 REMARK 3 CHIRALITY : 0.043 326 REMARK 3 PLANARITY : 0.005 412 REMARK 3 DIHEDRAL : 14.472 866 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4QBR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000085854. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19077 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09600 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.1M BIS-TRIS-HCL, PH REMARK 280 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, E 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 ASN A 611 REMARK 465 ASN C 611 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 O HOH A 894 O HOH A 896 2.14 REMARK 500 O HOH A 871 O HOH A 895 2.15 REMARK 500 O HOH A 846 O HOH A 870 2.16 REMARK 500 OE1 GLN C 527 O HOH C 838 2.16 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 484 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 484 NE - CZ - NH2 ANGL. DEV. = 3.3 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 C 554 -62.73 -121.42 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 LEU C 504 10.36 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 703 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 494 SG REMARK 620 2 CYS A 497 SG 113.8 REMARK 620 3 CYS A 514 SG 117.9 109.3 REMARK 620 4 CYS A 517 SG 104.2 106.0 104.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 537 SG REMARK 620 2 CYS A 540 SG 106.7 REMARK 620 3 CYS A 559 SG 113.3 111.9 REMARK 620 4 CYS A 562 SG 115.9 104.8 104.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 549 SG REMARK 620 2 CYS A 554 SG 109.7 REMARK 620 3 CYS A 583 SG 112.6 104.8 REMARK 620 4 CYS A 586 SG 107.2 104.5 117.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 703 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 494 SG REMARK 620 2 CYS C 497 SG 115.2 REMARK 620 3 CYS C 514 SG 115.7 109.2 REMARK 620 4 CYS C 517 SG 105.8 105.2 104.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 537 SG REMARK 620 2 CYS C 540 SG 109.2 REMARK 620 3 CYS C 559 SG 112.9 112.7 REMARK 620 4 CYS C 562 SG 111.6 106.8 103.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 549 SG REMARK 620 2 CYS C 554 SG 112.6 REMARK 620 3 CYS C 583 SG 112.0 105.1 REMARK 620 4 CYS C 586 SG 108.0 100.1 118.5 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 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 703 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QBS RELATED DB: PDB REMARK 900 RELATED ID: 4QBQ RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE OF THE ENTITY 2 OF THIS PROTEIN WAS NOT AVAILABLE AT REMARK 999 THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF REMARK 999 DEPOSITION. DBREF 4QBR A 476 611 UNP Q9Y6K1 DNM3A_HUMAN 476 611 DBREF 4QBR C 476 611 UNP Q9Y6K1 DNM3A_HUMAN 476 611 DBREF 4QBR P 1 7 PDB 4QBR 4QBR 1 7 DBREF 4QBR E 1 7 PDB 4QBR 4QBR 1 7 SEQADV 4QBR SER A 475 UNP Q9Y6K1 EXPRESSION TAG SEQADV 4QBR ASP A 550 UNP Q9Y6K1 GLY 550 ENGINEERED MUTATION SEQADV 4QBR SER C 475 UNP Q9Y6K1 EXPRESSION TAG SEQADV 4QBR ASP C 550 UNP Q9Y6K1 GLY 550 ENGINEERED MUTATION SEQRES 1 A 137 SER ARG GLU ARG LEU VAL TYR GLU VAL ARG GLN LYS CYS SEQRES 2 A 137 ARG ASN ILE GLU ASP ILE CYS ILE SER CYS GLY SER LEU SEQRES 3 A 137 ASN VAL THR LEU GLU HIS PRO LEU PHE VAL GLY GLY MET SEQRES 4 A 137 CYS GLN ASN CYS LYS ASN CYS PHE LEU GLU CYS ALA TYR SEQRES 5 A 137 GLN TYR ASP ASP ASP GLY TYR GLN SER TYR CYS THR ILE SEQRES 6 A 137 CYS CYS GLY GLY ARG GLU VAL LEU MET CYS ASP ASN ASN SEQRES 7 A 137 ASN CYS CYS ARG CYS PHE CYS VAL GLU CYS VAL ASP LEU SEQRES 8 A 137 LEU VAL GLY PRO GLY ALA ALA GLN ALA ALA ILE LYS GLU SEQRES 9 A 137 ASP PRO TRP ASN CYS TYR MET CYS GLY HIS LYS GLY THR SEQRES 10 A 137 TYR GLY LEU LEU ARG ARG ARG GLU ASP TRP PRO SER ARG SEQRES 11 A 137 LEU GLN MET PHE PHE ALA ASN SEQRES 1 P 7 ALA ARG THR LYS GLN THR ALA SEQRES 1 C 137 SER ARG GLU ARG LEU VAL TYR GLU VAL ARG GLN LYS CYS SEQRES 2 C 137 ARG ASN ILE GLU ASP ILE CYS ILE SER CYS GLY SER LEU SEQRES 3 C 137 ASN VAL THR LEU GLU HIS PRO LEU PHE VAL GLY GLY MET SEQRES 4 C 137 CYS GLN ASN CYS LYS ASN CYS PHE LEU GLU CYS ALA TYR SEQRES 5 C 137 GLN TYR ASP ASP ASP GLY TYR GLN SER TYR CYS THR ILE SEQRES 6 C 137 CYS CYS GLY GLY ARG GLU VAL LEU MET CYS ASP ASN ASN SEQRES 7 C 137 ASN CYS CYS ARG CYS PHE CYS VAL GLU CYS VAL ASP LEU SEQRES 8 C 137 LEU VAL GLY PRO GLY ALA ALA GLN ALA ALA ILE LYS GLU SEQRES 9 C 137 ASP PRO TRP ASN CYS TYR MET CYS GLY HIS LYS GLY THR SEQRES 10 C 137 TYR GLY LEU LEU ARG ARG ARG GLU ASP TRP PRO SER ARG SEQRES 11 C 137 LEU GLN MET PHE PHE ALA ASN SEQRES 1 E 7 ALA ARG THR LYS GLN THR ALA HET ZN A 701 1 HET ZN A 702 1 HET ZN A 703 1 HET ZN C 701 1 HET ZN C 702 1 HET ZN C 703 1 HETNAM ZN ZINC ION FORMUL 5 ZN 6(ZN 2+) FORMUL 11 HOH *216(H2 O) HELIX 1 1 SER A 475 GLN A 485 1 11 HELIX 2 2 ASN A 489 ILE A 493 5 5 HELIX 3 3 CYS A 514 ALA A 525 1 12 HELIX 4 4 VAL A 560 VAL A 567 1 8 HELIX 5 5 GLY A 570 GLU A 578 1 9 HELIX 6 6 ASP A 600 ALA A 610 1 11 HELIX 7 7 ARG C 476 GLN C 485 1 10 HELIX 8 8 ASN C 489 ILE C 493 5 5 HELIX 9 9 CYS C 514 ALA C 525 1 12 HELIX 10 10 VAL C 560 VAL C 567 1 8 HELIX 11 11 GLY C 570 GLU C 578 1 9 HELIX 12 12 ASP C 600 ALA C 610 1 11 SHEET 1 A 2 LEU A 504 GLU A 505 0 SHEET 2 A 2 GLY A 512 MET A 513 -1 O MET A 513 N LEU A 504 SHEET 1 B 3 CYS A 557 CYS A 559 0 SHEET 2 B 3 GLU A 545 MET A 548 -1 N LEU A 547 O PHE A 558 SHEET 3 B 3 ARG P 2 GLN P 5 -1 O LYS P 4 N VAL A 546 SHEET 1 C 2 THR A 591 TYR A 592 0 SHEET 2 C 2 LEU A 595 ARG A 596 -1 O LEU A 595 N TYR A 592 SHEET 1 D 2 LEU C 504 GLU C 505 0 SHEET 2 D 2 GLY C 512 MET C 513 -1 O MET C 513 N LEU C 504 SHEET 1 E 3 CYS C 557 CYS C 559 0 SHEET 2 E 3 GLU C 545 MET C 548 -1 N LEU C 547 O PHE C 558 SHEET 3 E 3 ARG E 2 GLN E 5 -1 O LYS E 4 N VAL C 546 SHEET 1 F 2 THR C 591 TYR C 592 0 SHEET 2 F 2 LEU C 595 ARG C 596 -1 O LEU C 595 N TYR C 592 LINK SG CYS A 494 ZN ZN A 703 1555 1555 2.36 LINK SG CYS A 497 ZN ZN A 703 1555 1555 2.25 LINK SG CYS A 514 ZN ZN A 703 1555 1555 2.39 LINK SG CYS A 517 ZN ZN A 703 1555 1555 2.44 LINK SG CYS A 537 ZN ZN A 702 1555 1555 2.39 LINK SG CYS A 540 ZN ZN A 702 1555 1555 2.41 LINK SG CYS A 549 ZN ZN A 701 1555 1555 2.22 LINK SG CYS A 554 ZN ZN A 701 1555 1555 2.36 LINK SG CYS A 559 ZN ZN A 702 1555 1555 2.22 LINK SG CYS A 562 ZN ZN A 702 1555 1555 2.32 LINK SG CYS A 583 ZN ZN A 701 1555 1555 2.32 LINK SG CYS A 586 ZN ZN A 701 1555 1555 2.32 LINK SG CYS C 494 ZN ZN C 703 1555 1555 2.36 LINK SG CYS C 497 ZN ZN C 703 1555 1555 2.28 LINK SG CYS C 514 ZN ZN C 703 1555 1555 2.45 LINK SG CYS C 517 ZN ZN C 703 1555 1555 2.36 LINK SG CYS C 537 ZN ZN C 702 1555 1555 2.37 LINK SG CYS C 540 ZN ZN C 702 1555 1555 2.33 LINK SG CYS C 549 ZN ZN C 701 1555 1555 2.23 LINK SG CYS C 554 ZN ZN C 701 1555 1555 2.46 LINK SG CYS C 559 ZN ZN C 702 1555 1555 2.28 LINK SG CYS C 562 ZN ZN C 702 1555 1555 2.35 LINK SG CYS C 583 ZN ZN C 701 1555 1555 2.31 LINK SG CYS C 586 ZN ZN C 701 1555 1555 2.41 CISPEP 1 ASP A 579 PRO A 580 0 5.72 CISPEP 2 ASP C 579 PRO C 580 0 5.43 SITE 1 AC1 4 CYS A 549 CYS A 554 CYS A 583 CYS A 586 SITE 1 AC2 4 CYS A 537 CYS A 540 CYS A 559 CYS A 562 SITE 1 AC3 4 CYS A 494 CYS A 497 CYS A 514 CYS A 517 SITE 1 AC4 4 CYS C 549 CYS C 554 CYS C 583 CYS C 586 SITE 1 AC5 4 CYS C 537 CYS C 540 CYS C 559 CYS C 562 SITE 1 AC6 4 CYS C 494 CYS C 497 CYS C 514 CYS C 517 CRYST1 36.057 37.161 50.125 78.70 83.89 81.56 P 1 2 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 0.027734 -0.004115 -0.002252 0.00000 SCALE2 0.000000 0.027205 -0.005074 0.00000 SCALE3 0.000000 0.000000 0.020410 0.00000