PDB Short entry for 4KZI HEADER TRANSCRIPTION 30-MAY-13 4KZI TITLE CRYSTAL STRUCTURE OF TR3 LBD IN COMPLEX WITH DPDO COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR RECEPTOR SUBFAMILY 4 GROUP A MEMBER 1; COMPND 3 CHAIN: B, A; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN, UNP RESIDUES 351-598; COMPND 5 SYNONYM: EARLY RESPONSE PROTEIN NAK1, NUCLEAR HORMONE RECEPTOR COMPND 6 NUR/77, NUR77, ORPHAN NUCLEAR RECEPTOR HMR, ORPHAN NUCLEAR RECEPTOR COMPND 7 TR3, ST-59, TESTICULAR RECEPTOR 3; 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: GFRP1, HMR, NAK1, NR4A1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS ORPHAN NUCLEAR RECEPTOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR F.LI,Q.ZHANG,A.LI,X.TIAN,Q.CAI,W.WANG,Y.WANG,H.CHEN,Y.XING,Q.WU,T.LIN REVDAT 4 20-MAR-24 4KZI 1 REMARK REVDAT 3 25-DEC-19 4KZI 1 JRNL SEQADV REVDAT 2 15-NOV-17 4KZI 1 REMARK REVDAT 1 18-DEC-13 4KZI 0 JRNL AUTH W.J.WANG,Y.WANG,H.Z.CHEN,Y.Z.XING,F.W.LI,Q.ZHANG,B.ZHOU, JRNL AUTH 2 H.K.ZHANG,J.ZHANG,X.L.BIAN,L.LI,Y.LIU,B.X.ZHAO,Y.CHEN,R.WU, JRNL AUTH 3 A.Z.LI,L.M.YAO,P.CHEN,Y.ZHANG,X.Y.TIAN,F.BEERMANN,M.WU, JRNL AUTH 4 J.HAN,P.Q.HUANG,T.LIN,Q.WU JRNL TITL ORPHAN NUCLEAR RECEPTOR TR3 ACTS IN AUTOPHAGIC CELL DEATH JRNL TITL 2 VIA MITOCHONDRIAL SIGNALING PATHWAY. JRNL REF NAT.CHEM.BIOL. V. 10 133 2014 JRNL REFN ESSN 1552-4469 JRNL PMID 24316735 JRNL DOI 10.1038/NCHEMBIO.1406 REMARK 2 REMARK 2 RESOLUTION. 2.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 29148 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1486 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) : 2.41 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.47 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1948 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 117 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3641 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 92 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.98000 REMARK 3 B22 (A**2) : 0.15000 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): 0.277 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.225 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.168 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.280 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3753 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3720 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5075 ; 1.787 ; 2.007 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8562 ; 1.219 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 461 ; 5.986 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 154 ;38.433 ;23.182 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 646 ;18.983 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;18.035 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 587 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4108 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 820 ; 0.005 ; 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 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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: REFINED INDIVIDUALLY REMARK 4 REMARK 4 4KZI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000079990. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 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) : 0.98 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29201 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.45500 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 (%): 61.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM CITRATE, GLYCEROL, PH REMARK 280 4.2, VAPOR DIFFUSION, TEMPERATURE 277K 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 37.36150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.45900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.25600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.45900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.36150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.25600 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 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 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: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 MET B 350 REMARK 465 SER B 351 REMARK 465 LYS B 352 REMARK 465 PRO B 353 REMARK 465 LYS B 354 REMARK 465 GLN B 355 REMARK 465 PRO B 356 REMARK 465 PRO B 357 REMARK 465 ASP B 358 REMARK 465 ALA B 359 REMARK 465 SER B 360 REMARK 465 PHE B 395 REMARK 465 GLY B 396 REMARK 465 GLN B 547 REMARK 465 PRO B 548 REMARK 465 LEU B 599 REMARK 465 GLU B 600 REMARK 465 HIS B 601 REMARK 465 HIS B 602 REMARK 465 HIS B 603 REMARK 465 HIS B 604 REMARK 465 HIS B 605 REMARK 465 HIS B 606 REMARK 465 MET A 350 REMARK 465 SER A 351 REMARK 465 LYS A 352 REMARK 465 PRO A 353 REMARK 465 LYS A 354 REMARK 465 GLN A 355 REMARK 465 PRO A 356 REMARK 465 PRO A 357 REMARK 465 ASP A 358 REMARK 465 ALA A 359 REMARK 465 SER A 360 REMARK 465 PRO A 361 REMARK 465 GLU A 545 REMARK 465 PRO A 546 REMARK 465 GLN A 547 REMARK 465 PRO A 548 REMARK 465 ALA A 549 REMARK 465 LEU A 599 REMARK 465 GLU A 600 REMARK 465 HIS A 601 REMARK 465 HIS A 602 REMARK 465 HIS A 603 REMARK 465 HIS A 604 REMARK 465 HIS A 605 REMARK 465 HIS A 606 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 ALA B 362 CB REMARK 470 LYS B 381 CG CD CE NZ REMARK 470 GLN B 388 CD OE1 NE2 REMARK 470 LYS B 397 CG CD CE NZ REMARK 470 GLU B 545 CG CD OE1 OE2 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 ALA B 549 OG SER B 553 2.09 REMARK 500 NH2 ARG A 370 OD1 ASP A 374 2.11 REMARK 500 OE1 GLU A 445 C9 ZJ0 A 703 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 OE1 GLU B 459 OD2 ASP A 580 3544 2.05 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 PRO B 393 C - N - CD ANGL. DEV. = -26.7 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 ALA B 362 -103.09 97.44 REMARK 500 GLU B 398 153.33 -45.31 REMARK 500 GLU B 545 -178.08 -54.13 REMARK 500 PRO B 597 35.71 -66.53 REMARK 500 THR A 379 -81.41 -48.72 REMARK 500 ALA A 380 103.25 -52.24 REMARK 500 LYS A 381 2.93 126.98 REMARK 500 PRO A 597 36.97 -70.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU B 392 PRO B 393 -38.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZJ0 A 703 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KZJ RELATED DB: PDB REMARK 900 RELATED ID: 4KZM RELATED DB: PDB REMARK 900 RELATED ID: 4JGV RELATED DB: PDB DBREF 4KZI B 351 598 UNP P22736 NR4A1_HUMAN 351 598 DBREF 4KZI A 351 598 UNP P22736 NR4A1_HUMAN 351 598 SEQADV 4KZI MET B 350 UNP P22736 EXPRESSION TAG SEQADV 4KZI LEU B 599 UNP P22736 EXPRESSION TAG SEQADV 4KZI GLU B 600 UNP P22736 EXPRESSION TAG SEQADV 4KZI HIS B 601 UNP P22736 EXPRESSION TAG SEQADV 4KZI HIS B 602 UNP P22736 EXPRESSION TAG SEQADV 4KZI HIS B 603 UNP P22736 EXPRESSION TAG SEQADV 4KZI HIS B 604 UNP P22736 EXPRESSION TAG SEQADV 4KZI HIS B 605 UNP P22736 EXPRESSION TAG SEQADV 4KZI HIS B 606 UNP P22736 EXPRESSION TAG SEQADV 4KZI MET A 350 UNP P22736 EXPRESSION TAG SEQADV 4KZI LEU A 599 UNP P22736 EXPRESSION TAG SEQADV 4KZI GLU A 600 UNP P22736 EXPRESSION TAG SEQADV 4KZI HIS A 601 UNP P22736 EXPRESSION TAG SEQADV 4KZI HIS A 602 UNP P22736 EXPRESSION TAG SEQADV 4KZI HIS A 603 UNP P22736 EXPRESSION TAG SEQADV 4KZI HIS A 604 UNP P22736 EXPRESSION TAG SEQADV 4KZI HIS A 605 UNP P22736 EXPRESSION TAG SEQADV 4KZI HIS A 606 UNP P22736 EXPRESSION TAG SEQRES 1 B 257 MET SER LYS PRO LYS GLN PRO PRO ASP ALA SER PRO ALA SEQRES 2 B 257 ASN LEU LEU THR SER LEU VAL ARG ALA HIS LEU ASP SER SEQRES 3 B 257 GLY PRO SER THR ALA LYS LEU ASP TYR SER LYS PHE GLN SEQRES 4 B 257 GLU LEU VAL LEU PRO HIS PHE GLY LYS GLU ASP ALA GLY SEQRES 5 B 257 ASP VAL GLN GLN PHE TYR ASP LEU LEU SER GLY SER LEU SEQRES 6 B 257 GLU VAL ILE ARG LYS TRP ALA GLU LYS ILE PRO GLY PHE SEQRES 7 B 257 ALA GLU LEU SER PRO ALA ASP GLN ASP LEU LEU LEU GLU SEQRES 8 B 257 SER ALA PHE LEU GLU LEU PHE ILE LEU ARG LEU ALA TYR SEQRES 9 B 257 ARG SER LYS PRO GLY GLU GLY LYS LEU ILE PHE CYS SER SEQRES 10 B 257 GLY LEU VAL LEU HIS ARG LEU GLN CYS ALA ARG GLY PHE SEQRES 11 B 257 GLY ASP TRP ILE ASP SER ILE LEU ALA PHE SER ARG SER SEQRES 12 B 257 LEU HIS SER LEU LEU VAL ASP VAL PRO ALA PHE ALA CYS SEQRES 13 B 257 LEU SER ALA LEU VAL LEU ILE THR ASP ARG HIS GLY LEU SEQRES 14 B 257 GLN GLU PRO ARG ARG VAL GLU GLU LEU GLN ASN ARG ILE SEQRES 15 B 257 ALA SER CYS LEU LYS GLU HIS VAL ALA ALA VAL ALA GLY SEQRES 16 B 257 GLU PRO GLN PRO ALA SER CYS LEU SER ARG LEU LEU GLY SEQRES 17 B 257 LYS LEU PRO GLU LEU ARG THR LEU CYS THR GLN GLY LEU SEQRES 18 B 257 GLN ARG ILE PHE TYR LEU LYS LEU GLU ASP LEU VAL PRO SEQRES 19 B 257 PRO PRO PRO ILE ILE ASP LYS ILE PHE MET ASP THR LEU SEQRES 20 B 257 PRO PHE LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 A 257 MET SER LYS PRO LYS GLN PRO PRO ASP ALA SER PRO ALA SEQRES 2 A 257 ASN LEU LEU THR SER LEU VAL ARG ALA HIS LEU ASP SER SEQRES 3 A 257 GLY PRO SER THR ALA LYS LEU ASP TYR SER LYS PHE GLN SEQRES 4 A 257 GLU LEU VAL LEU PRO HIS PHE GLY LYS GLU ASP ALA GLY SEQRES 5 A 257 ASP VAL GLN GLN PHE TYR ASP LEU LEU SER GLY SER LEU SEQRES 6 A 257 GLU VAL ILE ARG LYS TRP ALA GLU LYS ILE PRO GLY PHE SEQRES 7 A 257 ALA GLU LEU SER PRO ALA ASP GLN ASP LEU LEU LEU GLU SEQRES 8 A 257 SER ALA PHE LEU GLU LEU PHE ILE LEU ARG LEU ALA TYR SEQRES 9 A 257 ARG SER LYS PRO GLY GLU GLY LYS LEU ILE PHE CYS SER SEQRES 10 A 257 GLY LEU VAL LEU HIS ARG LEU GLN CYS ALA ARG GLY PHE SEQRES 11 A 257 GLY ASP TRP ILE ASP SER ILE LEU ALA PHE SER ARG SER SEQRES 12 A 257 LEU HIS SER LEU LEU VAL ASP VAL PRO ALA PHE ALA CYS SEQRES 13 A 257 LEU SER ALA LEU VAL LEU ILE THR ASP ARG HIS GLY LEU SEQRES 14 A 257 GLN GLU PRO ARG ARG VAL GLU GLU LEU GLN ASN ARG ILE SEQRES 15 A 257 ALA SER CYS LEU LYS GLU HIS VAL ALA ALA VAL ALA GLY SEQRES 16 A 257 GLU PRO GLN PRO ALA SER CYS LEU SER ARG LEU LEU GLY SEQRES 17 A 257 LYS LEU PRO GLU LEU ARG THR LEU CYS THR GLN GLY LEU SEQRES 18 A 257 GLN ARG ILE PHE TYR LEU LYS LEU GLU ASP LEU VAL PRO SEQRES 19 A 257 PRO PRO PRO ILE ILE ASP LYS ILE PHE MET ASP THR LEU SEQRES 20 A 257 PRO PHE LEU GLU HIS HIS HIS HIS HIS HIS HET GOL B 701 6 HET GOL A 701 6 HET GOL A 702 6 HET ZJ0 A 703 21 HETNAM GOL GLYCEROL HETNAM ZJ0 1-(3,5-DIMETHOXYPHENYL)DECAN-1-ONE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 3(C3 H8 O3) FORMUL 6 ZJ0 C18 H28 O3 FORMUL 7 HOH *92(H2 O) HELIX 1 1 ALA B 362 SER B 375 1 14 HELIX 2 2 ASP B 399 LYS B 423 1 25 HELIX 3 3 GLY B 426 LEU B 430 5 5 HELIX 4 4 SER B 431 SER B 455 1 25 HELIX 5 5 LYS B 456 GLU B 459 5 4 HELIX 6 6 ARG B 472 GLY B 480 1 9 HELIX 7 7 ASP B 481 LEU B 496 1 16 HELIX 8 8 ASP B 499 ILE B 512 1 14 HELIX 9 9 GLU B 520 VAL B 542 1 23 HELIX 10 10 SER B 550 GLY B 557 1 8 HELIX 11 11 GLY B 557 ASP B 580 1 24 HELIX 12 12 PRO B 585 LEU B 596 1 12 HELIX 13 13 ASN A 363 SER A 375 1 13 HELIX 14 14 ASP A 399 GLU A 422 1 24 HELIX 15 15 GLY A 426 LEU A 430 5 5 HELIX 16 16 SER A 431 SER A 455 1 25 HELIX 17 17 LYS A 456 GLU A 459 5 4 HELIX 18 18 ARG A 472 GLY A 480 1 9 HELIX 19 19 ASP A 481 LEU A 496 1 16 HELIX 20 20 ASP A 499 ILE A 512 1 14 HELIX 21 21 GLU A 520 GLY A 544 1 25 HELIX 22 22 CYS A 551 GLY A 557 1 7 HELIX 23 23 LYS A 558 ASP A 580 1 23 HELIX 24 24 PRO A 585 LEU A 596 1 12 SHEET 1 A 2 LYS B 461 ILE B 463 0 SHEET 2 A 2 VAL B 469 HIS B 471 -1 O LEU B 470 N LEU B 462 SHEET 1 B 2 LYS A 461 ILE A 463 0 SHEET 2 B 2 VAL A 469 HIS A 471 -1 O LEU A 470 N LEU A 462 CISPEP 1 PRO B 361 ALA B 362 0 -22.04 CISPEP 2 GLU B 545 PRO B 546 0 12.86 SITE 1 AC1 7 HIS B 372 SER B 375 GLY B 376 ARG B 450 SITE 2 AC1 7 ARG B 454 HOH B 813 HOH B 826 SITE 1 AC2 4 LEU A 509 VAL A 510 THR A 513 ZJ0 A 703 SITE 1 AC3 8 HIS A 372 SER A 375 GLY A 376 PRO A 377 SITE 2 AC3 8 ARG A 450 ARG A 454 HOH A 806 HOH A 812 SITE 1 AC4 15 SER A 441 ALA A 442 LEU A 444 GLU A 445 SITE 2 AC4 15 GLU A 459 VAL A 510 THR A 513 ASP A 514 SITE 3 AC4 15 ARG A 515 ARG A 563 CYS A 566 GOL A 701 SITE 4 AC4 15 HOH A 822 HOH A 826 HOH A 833 CRYST1 74.723 76.512 128.918 90.00 90.00 90.00 P 21 21 21 8 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 0.013383 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013070 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007757 0.00000